From f349e2ee90d7c3746373bb41ae26b2db3d363353 Mon Sep 17 00:00:00 2001 From: frankambrosio3 <64995676+frankambrosio3@users.noreply.github.com> Date: Wed, 26 Jan 2022 16:47:11 -0500 Subject: [PATCH] Sc2 val dev (#6) * Create compare_data_tables.py * fix white space * more pandas * import pdf kit, print df_diff_vert to pdf * added default for outfile basename * added pdfkit stuff * print basic html and pdf * Added excel output and pdf options * Drop columns that will almost always differ, keep only the columns that matter for validating the workflow * Print diffs count list to pdf Co-authored-by: Robert A. Petit III --- .../CDC_VOI_VOC_Lineages_v1-5-2.tsv | 17 +++ .../CDC_VOI_VOC_Lineages_v1-5-3.tsv | 17 +++ scripts/compare-data-tables.py | 141 ++++++++++++++++++ 3 files changed, 175 insertions(+) create mode 100644 reference_files/CDC_VOI_VOC_Lineages_v1-5-2.tsv create mode 100644 reference_files/CDC_VOI_VOC_Lineages_v1-5-3.tsv create mode 100755 scripts/compare-data-tables.py diff --git a/reference_files/CDC_VOI_VOC_Lineages_v1-5-2.tsv b/reference_files/CDC_VOI_VOC_Lineages_v1-5-2.tsv new file mode 100644 index 0000000..5f7c9cf --- /dev/null +++ b/reference_files/CDC_VOI_VOC_Lineages_v1-5-2.tsv @@ -0,0 +1,17 @@ +entity:CDC_VOI_VOC_Lineages_v1-5-2_id aligned_bai aligned_bam assembly_fasta assembly_length_unambiguous assembly_mean_coverage assembly_method auspice_json bbduk_docker bwa_version consensus_flagstat consensus_stats fastqc_clean1 fastqc_clean2 fastqc_clean_pairs fastqc_raw1 fastqc_raw2 fastqc_raw_pairs fastqc_version ivar_tsv ivar_variant_version ivar_vcf ivar_version_consensus ivar_version_primtrim kraken_human kraken_human_dehosted kraken_report kraken_report_dehosted kraken_sc2 kraken_sc2_dehosted kraken_version meanbaseq_trim meanmapq_trim nextclade_aa_dels nextclade_aa_subs nextclade_clade nextclade_json nextclade_tsv nextclade_version number_Degenerate number_N number_Total pango_lineage pango_lineage_report pangolin_assignment_version pangolin_conflicts pangolin_docker pangolin_notes pangolin_versions percent_reference_coverage primer_bed_name primer_trimmed_read_percent read1_clean read1_dehosted read2_clean read2_dehosted read_1 read_2 samtools_version samtools_version_consensus samtools_version_primtrim samtools_version_stats seq_platform titan_illumina_pe_analysis_date titan_illumina_pe_version trimmomatic_version vadr_alerts_list vadr_docker vadr_num_alerts +hCoV-19_England_CAMC-13E7537_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-consensus/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.ivar.consensus.fasta 29287 1714.52 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-nextclade_one_sample/hCoV-19_England_CAMC-13E7537_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.stats.txt 163069 163069 163069 217320 216830 Uneven pairs: R1=217320, R2=216830 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-variant_call/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-variant_call/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-read_QC_trim/read_QC_trim/340aef6d-c5ee-4257-a3a2-cf5eaf5c4e16/call-kraken2_raw/cacheCopy/hCoV-19_England_CAMC-13E7537_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-read_QC_trim/read_QC_trim/340aef6d-c5ee-4257-a3a2-cf5eaf5c4e16/call-kraken2_dehosted/cacheCopy/hCoV-19_England_CAMC-13E7537_2021_kraken2_report.txt 99.66 99.66 Kraken version 2.0.8-beta 36.4 60 ORF1a:S3675-,ORF1a:G3676-,ORF1a:F3677- N:P80R,N:R203K,N:G204R,N:D348H,ORF1a:S1188L,ORF1a:K1795Q,ORF1a:D3526N,ORF1b:P314L,ORF1b:E1264D,ORF3a:S253P,ORF8:E92K,ORF9b:Q77E,S:L18F,S:T20N,S:P26S,S:D138Y,S:R190S,S:K417T,S:E484K,S:N501Y,S:D614G,S:H655Y,S:T1027I 20J (Gamma, V3) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-nextclade_one_sample/hCoV-19_England_CAMC-13E7537_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-nextclade_one_sample/hCoV-19_England_CAMC-13E7537_2021.ivar.consensus.nextclade.tsv 1.9.0 0 515 29802 P.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-pangolin3/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 14; Ref alleles 0; Amb alleles 0; Usher placements: P.1(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 97.94 V3_nCoV-2019.primer.bed 99.01 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-read_QC_trim/read_QC_trim/340aef6d-c5ee-4257-a3a2-cf5eaf5c4e16/call-bbduk/cacheCopy/hCoV-19_England_CAMC-13E7537_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-read_QC_trim/read_QC_trim/340aef6d-c5ee-4257-a3a2-cf5eaf5c4e16/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-13E7537_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-read_QC_trim/read_QC_trim/340aef6d-c5ee-4257-a3a2-cf5eaf5c4e16/call-bbduk/cacheCopy/hCoV-19_England_CAMC-13E7537_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-read_QC_trim/read_QC_trim/340aef6d-c5ee-4257-a3a2-cf5eaf5c4e16/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-13E7537_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-13E7537_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-13E7537_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-vadr/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.ivar.consensus/hCoV-19_England_CAMC-13E7537_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_England_CAMC-14E726C_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-consensus/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.ivar.consensus.fasta 29238 1167.1 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-nextclade_one_sample/hCoV-19_England_CAMC-14E726C_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.stats.txt 116979 116979 116979 198715 198332 Uneven pairs: R1=198715, R2=198332 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-variant_call/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-variant_call/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0.01 0.01 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-read_QC_trim/read_QC_trim/71f2f07a-75c3-4e91-b388-e1eafe9d6f8b/call-kraken2_raw/cacheCopy/hCoV-19_England_CAMC-14E726C_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-read_QC_trim/read_QC_trim/71f2f07a-75c3-4e91-b388-e1eafe9d6f8b/call-kraken2_dehosted/cacheCopy/hCoV-19_England_CAMC-14E726C_2021_kraken2_report.txt 79.23 79.23 Kraken version 2.0.8-beta 36.4 60 NA M:I82S,N:R203M,N:D377Y,ORF1a:T1241I,ORF1a:T1567I,ORF1a:T3646A,ORF1b:P314L,ORF1b:G1129C,ORF1b:M1352I,ORF1b:M1581I,ORF1b:K2310R,ORF1b:S2312A,ORF3a:S26L,ORF7a:V82A,S:T95I,S:G142D,S:E154K,S:L452R,S:E484Q,S:D614G,S:P681R,S:Q1071H 21B (Kappa) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-nextclade_one_sample/hCoV-19_England_CAMC-14E726C_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-nextclade_one_sample/hCoV-19_England_CAMC-14E726C_2021.ivar.consensus.nextclade.tsv 1.9.0 0 567 29805 B.1.617.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-pangolin3/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 11; Ref alleles 0; Amb alleles 0; Usher placements: B.1.617.1(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 97.78 V3_nCoV-2019.primer.bed 99.4 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-read_QC_trim/read_QC_trim/71f2f07a-75c3-4e91-b388-e1eafe9d6f8b/call-bbduk/cacheCopy/hCoV-19_England_CAMC-14E726C_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-read_QC_trim/read_QC_trim/71f2f07a-75c3-4e91-b388-e1eafe9d6f8b/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-14E726C_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-read_QC_trim/read_QC_trim/71f2f07a-75c3-4e91-b388-e1eafe9d6f8b/call-bbduk/cacheCopy/hCoV-19_England_CAMC-14E726C_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-read_QC_trim/read_QC_trim/71f2f07a-75c3-4e91-b388-e1eafe9d6f8b/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-14E726C_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-14E726C_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-14E726C_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-vadr/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.ivar.consensus/hCoV-19_England_CAMC-14E726C_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_England_CAMC-14E7A0A_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-consensus/hCoV-19_England_CAMC-14E7A0A_2021.ivar.consensus.fasta 29794 15954.5 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-nextclade_one_sample/hCoV-19_England_CAMC-14E7A0A_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021.stats.txt 1478767 1478767 1478767 1893395 1890185 Uneven pairs: R1=1893395, R2=1890185 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-variant_call/hCoV-19_England_CAMC-14E7A0A_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-variant_call/hCoV-19_England_CAMC-14E7A0A_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-read_QC_trim/read_QC_trim/aa3dd91d-b30f-4ae6-abb4-aac1fddda110/call-kraken2_raw/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-read_QC_trim/read_QC_trim/aa3dd91d-b30f-4ae6-abb4-aac1fddda110/call-kraken2_dehosted/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021_kraken2_report.txt 100 100 Kraken version 2.0.8-beta 36.4 60 ORF8:D119-,ORF8:F120-,S:E156-,S:F157- M:I82T,N:D63G,N:R203M,N:G215C,N:D377Y,ORF1a:A1306S,ORF1a:P2046L,ORF1a:P2287S,ORF1a:V2930L,ORF1a:T3255I,ORF1a:T3646A,ORF1b:P314L,ORF1b:G662S,ORF1b:P1000L,ORF1b:A1918V,ORF3a:S26L,ORF7a:V82A,ORF7a:T120I,ORF7b:T40I,ORF9b:T60A,S:T19R,S:G142D,S:R158G,S:L452R,S:T478K,S:D614G,S:P681R,S:D950N 21J (Delta) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-nextclade_one_sample/hCoV-19_England_CAMC-14E7A0A_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-nextclade_one_sample/hCoV-19_England_CAMC-14E7A0A_2021.ivar.consensus.nextclade.tsv 1.9.0 0 58 29852 B.1.617.2 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-pangolin3/hCoV-19_England_CAMC-14E7A0A_2021.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.64 V3_nCoV-2019.primer.bed 99.9 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-read_QC_trim/read_QC_trim/aa3dd91d-b30f-4ae6-abb4-aac1fddda110/call-bbduk/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-read_QC_trim/read_QC_trim/aa3dd91d-b30f-4ae6-abb4-aac1fddda110/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-read_QC_trim/read_QC_trim/aa3dd91d-b30f-4ae6-abb4-aac1fddda110/call-bbduk/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-read_QC_trim/read_QC_trim/aa3dd91d-b30f-4ae6-abb4-aac1fddda110/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-14E7A0A_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-14E7A0A_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-vadr/hCoV-19_England_CAMC-14E7A0A_2021.ivar.consensus/hCoV-19_England_CAMC-14E7A0A_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_England_CAMC-1510779_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-1510779_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-1510779_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-consensus/cacheCopy/hCoV-19_England_CAMC-1510779_2021.ivar.consensus.fasta 29513 8814.18 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-nextclade_one_sample/hCoV-19_England_CAMC-1510779_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-1510779_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-1510779_2021.stats.txt 849766 849766 849766 1113379 1111258 Uneven pairs: R1=1113379, R2=1111258 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-variant_call/cacheCopy/hCoV-19_England_CAMC-1510779_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-variant_call/cacheCopy/hCoV-19_England_CAMC-1510779_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-read_QC_trim/read_QC_trim/bf546401-91fc-4cba-b351-ffe98e11c894/call-kraken2_raw/cacheCopy/hCoV-19_England_CAMC-1510779_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-read_QC_trim/read_QC_trim/bf546401-91fc-4cba-b351-ffe98e11c894/call-kraken2_dehosted/cacheCopy/hCoV-19_England_CAMC-1510779_2021_kraken2_report.txt 99.99 99.99 Kraken version 2.0.8-beta 36.4 60 NA M:I82S,N:R203M,N:D377Y,ORF1a:T1567I,ORF1a:T3646A,ORF1b:T17I,ORF1b:P314L,ORF1b:G1129C,ORF1b:M1352I,ORF1b:K2310R,ORF1b:S2312A,ORF3a:S26L,ORF7a:V82A,S:T95I,S:G142D,S:E154K,S:L452R,S:E484Q,S:D614G,S:P681R,S:Q1071H 21B (Kappa) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-nextclade_one_sample/hCoV-19_England_CAMC-1510779_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-nextclade_one_sample/hCoV-19_England_CAMC-1510779_2021.ivar.consensus.nextclade.tsv 1.9.0 0 292 29805 B.1.617.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-pangolin3/cacheCopy/hCoV-19_England_CAMC-1510779_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 11; Ref alleles 0; Amb alleles 0; Usher placements: B.1.617.1(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 98.7 V3_nCoV-2019.primer.bed 99.88 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-read_QC_trim/read_QC_trim/bf546401-91fc-4cba-b351-ffe98e11c894/call-bbduk/cacheCopy/hCoV-19_England_CAMC-1510779_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-read_QC_trim/read_QC_trim/bf546401-91fc-4cba-b351-ffe98e11c894/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-1510779_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-read_QC_trim/read_QC_trim/bf546401-91fc-4cba-b351-ffe98e11c894/call-bbduk/cacheCopy/hCoV-19_England_CAMC-1510779_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-read_QC_trim/read_QC_trim/bf546401-91fc-4cba-b351-ffe98e11c894/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-1510779_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-1510779_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-1510779_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-vadr/cacheCopy/hCoV-19_England_CAMC-1510779_2021.ivar.consensus/hCoV-19_England_CAMC-1510779_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_England_QEUH-14A3615_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-primer_trim/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-primer_trim/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-consensus/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.ivar.consensus.fasta 29610 14008.5 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-nextclade_one_sample/hCoV-19_England_QEUH-14A3615_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-stats_n_coverage/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-stats_n_coverage/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.stats.txt 1303647 1303647 1303647 1738634 1735175 Uneven pairs: R1=1738634, R2=1735175 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-variant_call/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-variant_call/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-read_QC_trim/read_QC_trim/b1940cba-d064-4812-8677-2f9e852ac76f/call-kraken2_raw/cacheCopy/hCoV-19_England_QEUH-14A3615_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-read_QC_trim/read_QC_trim/b1940cba-d064-4812-8677-2f9e852ac76f/call-kraken2_dehosted/cacheCopy/hCoV-19_England_QEUH-14A3615_2021_kraken2_report.txt 100 100 Kraken version 2.0.8-beta 36.4 60 ORF1a:S3675-,ORF1a:G3676-,ORF1a:F3677-,S:L241-,S:L242-,S:A243- E:P71L,N:T205I,ORF1a:T265I,ORF1a:K1655N,ORF1a:T2069I,ORF1a:K3353R,ORF1b:P314L,ORF1b:T1511I,ORF3a:Q57H,ORF3a:S171L,ORF8:I121L,S:D80A,S:D215G,S:K417N,S:E484K,S:N501Y,S:D614G,S:A701V 20H (Beta, V2) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-nextclade_one_sample/hCoV-19_England_QEUH-14A3615_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-nextclade_one_sample/hCoV-19_England_QEUH-14A3615_2021.ivar.consensus.nextclade.tsv 1.9.0 0 234 29844 B.1.351 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-pangolin3/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 12; Ref alleles 0; Amb alleles 0; Usher placements: B.1.351(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.02 V3_nCoV-2019.primer.bed 99.84 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-read_QC_trim/read_QC_trim/b1940cba-d064-4812-8677-2f9e852ac76f/call-bbduk/cacheCopy/hCoV-19_England_QEUH-14A3615_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-read_QC_trim/read_QC_trim/b1940cba-d064-4812-8677-2f9e852ac76f/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_QEUH-14A3615_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-read_QC_trim/read_QC_trim/b1940cba-d064-4812-8677-2f9e852ac76f/call-bbduk/cacheCopy/hCoV-19_England_QEUH-14A3615_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-read_QC_trim/read_QC_trim/b1940cba-d064-4812-8677-2f9e852ac76f/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_QEUH-14A3615_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_QEUH-14A3615_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_QEUH-14A3615_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-vadr/hCoV-19_England_QEUH-14A3615_2021.ivar.consensus/hCoV-19_England_QEUH-14A3615_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_England_QEUH-E93AAC_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-primer_trim/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-primer_trim/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-consensus/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.ivar.consensus.fasta 29733 8331.92 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-nextclade_one_sample/hCoV-19_England_QEUH-E93AAC_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-stats_n_coverage/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-stats_n_coverage/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.stats.txt 756413 756413 756413 915559 912627 Uneven pairs: R1=915559, R2=912627 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-variant_call/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-variant_call/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-read_QC_trim/read_QC_trim/69740b61-1a23-4c7b-bdf6-589abb6c01ac/call-kraken2_raw/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-read_QC_trim/read_QC_trim/69740b61-1a23-4c7b-bdf6-589abb6c01ac/call-kraken2_dehosted/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021_kraken2_report.txt 99.99 99.99 Kraken version 2.0.8-beta 36.5 60 N:M1-,ORF1a:S3675-,ORF1a:G3676-,ORF1a:F3677-,ORF6:M1-,S:H69-,S:V70-,S:Y144- E:L21F,M:I82T,N:S2M,N:D3Y,N:A12G,N:T205I,ORF1a:T2007I,ORF1b:P314F,ORF1b:D1735N,ORF6:F2M,ORF8:G8V,ORF9b:H9D,S:Q52R,S:A67V,S:E484K,S:D614G,S:Q677H,S:F888L 21D (Eta) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-nextclade_one_sample/hCoV-19_England_QEUH-E93AAC_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-nextclade_one_sample/hCoV-19_England_QEUH-E93AAC_2021.ivar.consensus.nextclade.tsv 1.9.0 0 0 29733 B.1.525 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-pangolin3/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.43 V3_nCoV-2019.primer.bed 99.89 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-read_QC_trim/read_QC_trim/69740b61-1a23-4c7b-bdf6-589abb6c01ac/call-bbduk/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-read_QC_trim/read_QC_trim/69740b61-1a23-4c7b-bdf6-589abb6c01ac/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-read_QC_trim/read_QC_trim/69740b61-1a23-4c7b-bdf6-589abb6c01ac/call-bbduk/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-read_QC_trim/read_QC_trim/69740b61-1a23-4c7b-bdf6-589abb6c01ac/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_QEUH-E93AAC_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_QEUH-E93AAC_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-vadr/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.ivar.consensus/hCoV-19_England_QEUH-E93AAC_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_England_QEUH-E948CF_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-primer_trim/cacheCopy/hCoV-19_England_QEUH-E948CF_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-primer_trim/cacheCopy/hCoV-19_England_QEUH-E948CF_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-consensus/cacheCopy/hCoV-19_England_QEUH-E948CF_2021.ivar.consensus.fasta 29759 13302 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-nextclade_one_sample/hCoV-19_England_QEUH-E948CF_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-stats_n_coverage/cacheCopy/hCoV-19_England_QEUH-E948CF_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-stats_n_coverage/cacheCopy/hCoV-19_England_QEUH-E948CF_2021.stats.txt 1208467 1208467 1208467 1507565 1500580 Uneven pairs: R1=1507565, R2=1500580 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-variant_call/cacheCopy/hCoV-19_England_QEUH-E948CF_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-variant_call/cacheCopy/hCoV-19_England_QEUH-E948CF_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-read_QC_trim/read_QC_trim/0100ef85-42b9-46d4-80d1-be8fcd09672a/call-kraken2_raw/cacheCopy/hCoV-19_England_QEUH-E948CF_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-read_QC_trim/read_QC_trim/0100ef85-42b9-46d4-80d1-be8fcd09672a/call-kraken2_dehosted/cacheCopy/hCoV-19_England_QEUH-E948CF_2021_kraken2_report.txt 100 100 Kraken version 2.0.8-beta 36.5 60 N:M1-,ORF1a:S3675-,ORF1a:G3676-,ORF1a:F3677-,ORF6:M1-,S:H69-,S:V70-,S:Y144- E:L21F,M:I82T,N:S2M,N:D3Y,N:A12G,N:T205I,ORF1a:T2007I,ORF1b:P314F,ORF1b:D1735N,ORF6:F2M,ORF8:G8V,ORF9b:H9D,S:Q52R,S:A67V,S:E484K,S:D614G,S:Q677H,S:F888L 21D (Eta) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-nextclade_one_sample/hCoV-19_England_QEUH-E948CF_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-nextclade_one_sample/hCoV-19_England_QEUH-E948CF_2021.ivar.consensus.nextclade.tsv 1.9.0 0 33 29792 B.1.525 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-pangolin3/hCoV-19_England_QEUH-E948CF_2021.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.52 V3_nCoV-2019.primer.bed 99.88 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-read_QC_trim/read_QC_trim/0100ef85-42b9-46d4-80d1-be8fcd09672a/call-bbduk/cacheCopy/hCoV-19_England_QEUH-E948CF_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-read_QC_trim/read_QC_trim/0100ef85-42b9-46d4-80d1-be8fcd09672a/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_QEUH-E948CF_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-read_QC_trim/read_QC_trim/0100ef85-42b9-46d4-80d1-be8fcd09672a/call-bbduk/cacheCopy/hCoV-19_England_QEUH-E948CF_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-read_QC_trim/read_QC_trim/0100ef85-42b9-46d4-80d1-be8fcd09672a/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_QEUH-E948CF_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_QEUH-E948CF_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_QEUH-E948CF_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-vadr/hCoV-19_England_QEUH-E948CF_2021.ivar.consensus/hCoV-19_England_QEUH-E948CF_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_England_RAND-14DD366_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-primer_trim/cacheCopy/hCoV-19_England_RAND-14DD366_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-primer_trim/cacheCopy/hCoV-19_England_RAND-14DD366_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-consensus/hCoV-19_England_RAND-14DD366_2021.ivar.consensus.fasta 29806 19422.1 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-nextclade_one_sample/hCoV-19_England_RAND-14DD366_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-stats_n_coverage/cacheCopy/hCoV-19_England_RAND-14DD366_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-stats_n_coverage/cacheCopy/hCoV-19_England_RAND-14DD366_2021.stats.txt 1818270 1818270 1818270 2326577 2323879 Uneven pairs: R1=2326577, R2=2323879 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-variant_call/hCoV-19_England_RAND-14DD366_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-variant_call/hCoV-19_England_RAND-14DD366_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-read_QC_trim/read_QC_trim/1cd92919-9ea9-4360-b380-2f6f51b9d127/call-kraken2_raw/cacheCopy/hCoV-19_England_RAND-14DD366_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-read_QC_trim/read_QC_trim/1cd92919-9ea9-4360-b380-2f6f51b9d127/call-kraken2_dehosted/cacheCopy/hCoV-19_England_RAND-14DD366_2021_kraken2_report.txt 100 100 Kraken version 2.0.8-beta 36.4 60 ORF8:D119-,ORF8:F120-,S:E156-,S:F157- M:I82T,N:D63G,N:R203M,N:G215C,N:D377Y,ORF1a:A1306S,ORF1a:P2046L,ORF1a:P2287S,ORF1a:V2930L,ORF1a:T3255I,ORF1a:T3646A,ORF1b:P314L,ORF1b:G662S,ORF1b:P1000L,ORF1b:A1918V,ORF3a:S26L,ORF7a:V82A,ORF7a:T120I,ORF7b:T40I,ORF9b:T60A,S:T19R,S:G142D,S:R158G,S:L452R,S:T478K,S:D614G,S:P681R,S:D950N 21J (Delta) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-nextclade_one_sample/hCoV-19_England_RAND-14DD366_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-nextclade_one_sample/hCoV-19_England_RAND-14DD366_2021.ivar.consensus.nextclade.tsv 1.9.0 0 51 29857 B.1.617.2 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-pangolin3/hCoV-19_England_RAND-14DD366_2021.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.68 V3_nCoV-2019.primer.bed 99.82 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-read_QC_trim/read_QC_trim/1cd92919-9ea9-4360-b380-2f6f51b9d127/call-bbduk/cacheCopy/hCoV-19_England_RAND-14DD366_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-read_QC_trim/read_QC_trim/1cd92919-9ea9-4360-b380-2f6f51b9d127/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_RAND-14DD366_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-read_QC_trim/read_QC_trim/1cd92919-9ea9-4360-b380-2f6f51b9d127/call-bbduk/cacheCopy/hCoV-19_England_RAND-14DD366_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-read_QC_trim/read_QC_trim/1cd92919-9ea9-4360-b380-2f6f51b9d127/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_RAND-14DD366_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_RAND-14DD366_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_RAND-14DD366_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-vadr/hCoV-19_England_RAND-14DD366_2021.ivar.consensus/hCoV-19_England_RAND-14DD366_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_USA_CA-QDX-2761_2020 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-primer_trim/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-primer_trim/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-consensus/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.ivar.consensus.fasta 29702 1242.74 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-nextclade_one_sample/hCoV-19_USA_CA-QDX-2761_2020.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-stats_n_coverage/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-stats_n_coverage/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.stats.txt 95702 95702 95702 146635 146635 146635 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-variant_call/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-variant_call/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0.2 0.07 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-read_QC_trim/read_QC_trim/c862bce2-093e-4cfe-be2a-754eed06ca72/call-kraken2_raw/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-read_QC_trim/read_QC_trim/c862bce2-093e-4cfe-be2a-754eed06ca72/call-kraken2_dehosted/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020_kraken2_report.txt 96.74 96.74 Kraken version 2.0.8-beta 37.6 60 NA N:T205I,ORF1a:R77L,ORF1a:T265I,ORF1a:S3158T,ORF1b:P314L,ORF1b:P976L,ORF1b:D1183Y,ORF3a:Q57H,S:S13I,S:W152C,S:L452R,S:D614G 21C (Epsilon) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-nextclade_one_sample/hCoV-19_USA_CA-QDX-2761_2020.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-nextclade_one_sample/hCoV-19_USA_CA-QDX-2761_2020.ivar.consensus.nextclade.tsv 1.9.0 0 104 29806 B.1.427 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-pangolin3/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.33 V3_nCoV-2019.primer.bed 96.08 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-read_QC_trim/read_QC_trim/c862bce2-093e-4cfe-be2a-754eed06ca72/call-bbduk/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-read_QC_trim/read_QC_trim/c862bce2-093e-4cfe-be2a-754eed06ca72/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-read_QC_trim/read_QC_trim/c862bce2-093e-4cfe-be2a-754eed06ca72/call-bbduk/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-read_QC_trim/read_QC_trim/c862bce2-093e-4cfe-be2a-754eed06ca72/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_CA-QDX-2761_2020_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_CA-QDX-2761_2020_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-vadr/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.ivar.consensus/hCoV-19_USA_CA-QDX-2761_2020.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_USA_CA-QDX-2781_2020 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-primer_trim/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-primer_trim/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-consensus/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.ivar.consensus.fasta 29559 608.594 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-nextclade_one_sample/hCoV-19_USA_CA-QDX-2781_2020.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-stats_n_coverage/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-stats_n_coverage/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.stats.txt 47611 47611 47611 76082 76082 76082 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-variant_call/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-variant_call/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0.06 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-read_QC_trim/read_QC_trim/185061c1-fdaf-403b-87aa-1b9e8156b2e4/call-kraken2_raw/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-read_QC_trim/read_QC_trim/185061c1-fdaf-403b-87aa-1b9e8156b2e4/call-kraken2_dehosted/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020_kraken2_report.txt 97.38 97.38 Kraken version 2.0.8-beta 37.6 60 NA N:T205I,ORF1a:T265I,ORF1a:A1473V,ORF1a:H2125Y,ORF1a:V3595G,ORF1a:F3789L,ORF1a:C3790F,ORF1a:I4205V,ORF1b:P314L,ORF1b:D1183Y,ORF1b:T2537I,ORF3a:Q57H,S:S13I,S:W152C,S:L452R,S:D614G 21C (Epsilon) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-nextclade_one_sample/hCoV-19_USA_CA-QDX-2781_2020.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-nextclade_one_sample/hCoV-19_USA_CA-QDX-2781_2020.ivar.consensus.nextclade.tsv 1.9.0 0 265 29824 B.1.429 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-pangolin3/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 98.85 V3_nCoV-2019.primer.bed 96.58 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-read_QC_trim/read_QC_trim/185061c1-fdaf-403b-87aa-1b9e8156b2e4/call-bbduk/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-read_QC_trim/read_QC_trim/185061c1-fdaf-403b-87aa-1b9e8156b2e4/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-read_QC_trim/read_QC_trim/185061c1-fdaf-403b-87aa-1b9e8156b2e4/call-bbduk/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-read_QC_trim/read_QC_trim/185061c1-fdaf-403b-87aa-1b9e8156b2e4/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_CA-QDX-2781_2020_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_CA-QDX-2781_2020_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-vadr/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.ivar.consensus/hCoV-19_USA_CA-QDX-2781_2020.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_USA_MA-QDX-2966_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-primer_trim/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-primer_trim/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-consensus/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.ivar.consensus.fasta 29807 802.693 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-nextclade_one_sample/hCoV-19_USA_MA-QDX-2966_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-stats_n_coverage/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-stats_n_coverage/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.stats.txt 56291 56291 56291 73899 73899 73899 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-variant_call/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-variant_call/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 1.9 0.53 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-read_QC_trim/read_QC_trim/2d8be66e-6d1c-4c75-b8be-f6ef4e5b3dfd/call-kraken2_raw/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-read_QC_trim/read_QC_trim/2d8be66e-6d1c-4c75-b8be-f6ef4e5b3dfd/call-kraken2_dehosted/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021_kraken2_report.txt 91.8 91.8 Kraken version 2.0.8-beta 37.8 60 NA N:A119S,N:R203K,N:G204R,N:M234I,ORF1a:L3468V,ORF1a:L3930F,ORF1b:P314L,ORF1b:T2432I,S:E484K,S:D614G,S:V1176F 20B gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-nextclade_one_sample/hCoV-19_USA_MA-QDX-2966_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-nextclade_one_sample/hCoV-19_USA_MA-QDX-2966_2021.ivar.consensus.nextclade.tsv 1.9.0 0 26 29833 P.2 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-pangolin3/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.68 V3_nCoV-2019.primer.bed 95.72 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-read_QC_trim/read_QC_trim/2d8be66e-6d1c-4c75-b8be-f6ef4e5b3dfd/call-bbduk/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-read_QC_trim/read_QC_trim/2d8be66e-6d1c-4c75-b8be-f6ef4e5b3dfd/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-read_QC_trim/read_QC_trim/2d8be66e-6d1c-4c75-b8be-f6ef4e5b3dfd/call-bbduk/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-read_QC_trim/read_QC_trim/2d8be66e-6d1c-4c75-b8be-f6ef4e5b3dfd/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_MA-QDX-2966_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_MA-QDX-2966_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-vadr/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.ivar.consensus/hCoV-19_USA_MA-QDX-2966_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_USA_NV-QDX-4024_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-primer_trim/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-primer_trim/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-consensus/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.ivar.consensus.fasta 29806 972.978 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-nextclade_one_sample/hCoV-19_USA_NV-QDX-4024_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-stats_n_coverage/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-stats_n_coverage/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.stats.txt 69643 69643 69643 92107 92107 92107 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-variant_call/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-variant_call/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0.07 0.02 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-read_QC_trim/read_QC_trim/f959c14e-c07f-46ce-9a99-ab03cac6e55f/call-kraken2_raw/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-read_QC_trim/read_QC_trim/f959c14e-c07f-46ce-9a99-ab03cac6e55f/call-kraken2_dehosted/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021_kraken2_report.txt 95.28 95.28 Kraken version 2.0.8-beta 37.7 60 NA N:A119S,N:R203K,N:G204R,N:M234I,ORF1a:L3468V,ORF1a:L3930F,ORF1a:T4249I,ORF1b:P314L,S:E484K,S:D614G,S:V1176F 20B gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-nextclade_one_sample/hCoV-19_USA_NV-QDX-4024_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-nextclade_one_sample/hCoV-19_USA_NV-QDX-4024_2021.ivar.consensus.nextclade.tsv 1.9.0 0 18 29824 P.2 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-pangolin3/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.68 V3_nCoV-2019.primer.bed 96.98 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-read_QC_trim/read_QC_trim/f959c14e-c07f-46ce-9a99-ab03cac6e55f/call-bbduk/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-read_QC_trim/read_QC_trim/f959c14e-c07f-46ce-9a99-ab03cac6e55f/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-read_QC_trim/read_QC_trim/f959c14e-c07f-46ce-9a99-ab03cac6e55f/call-bbduk/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-read_QC_trim/read_QC_trim/f959c14e-c07f-46ce-9a99-ab03cac6e55f/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_NV-QDX-4024_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_NV-QDX-4024_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-vadr/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.ivar.consensus/hCoV-19_USA_NV-QDX-4024_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_USA_RI-QDX-3232_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-primer_trim/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-primer_trim/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-consensus/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.ivar.consensus.fasta 29796 1091.8 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-nextclade_one_sample/hCoV-19_USA_RI-QDX-3232_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-stats_n_coverage/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-stats_n_coverage/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.stats.txt 82348 82348 82348 102908 102908 102908 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-variant_call/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-variant_call/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0.01 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-read_QC_trim/read_QC_trim/1265ab8d-f615-43af-93ed-f50ab52d507d/call-kraken2_raw/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-read_QC_trim/read_QC_trim/1265ab8d-f615-43af-93ed-f50ab52d507d/call-kraken2_dehosted/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021_kraken2_report.txt 97.04 97.04 Kraken version 2.0.8-beta 37.6 60 ORF1a:S3675-,ORF1a:G3676-,ORF1a:F3677- N:P199L,N:M234I,ORF1a:T265I,ORF1a:L3201P,ORF1b:P314L,ORF1b:Q813H,ORF1b:Q1011H,ORF3a:P42L,ORF3a:Q57H,ORF8:T11I,S:L5F,S:T95I,S:D253G,S:E484K,S:D614G,S:A701V 21F (Iota) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-nextclade_one_sample/hCoV-19_USA_RI-QDX-3232_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-nextclade_one_sample/hCoV-19_USA_RI-QDX-3232_2021.ivar.consensus.nextclade.tsv 1.9.0 0 28 29824 B.1.526 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-pangolin3/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 19; Ref alleles 4; Amb alleles 0; Usher placements: B.1.526(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.64 V3_nCoV-2019.primer.bed 96.75 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-read_QC_trim/read_QC_trim/1265ab8d-f615-43af-93ed-f50ab52d507d/call-bbduk/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-read_QC_trim/read_QC_trim/1265ab8d-f615-43af-93ed-f50ab52d507d/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-read_QC_trim/read_QC_trim/1265ab8d-f615-43af-93ed-f50ab52d507d/call-bbduk/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-read_QC_trim/read_QC_trim/1265ab8d-f615-43af-93ed-f50ab52d507d/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_RI-QDX-3232_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_RI-QDX-3232_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-vadr/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.ivar.consensus/hCoV-19_USA_RI-QDX-3232_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_USA_TX-DSHS-2263_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-primer_trim/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-primer_trim/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-consensus/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.ivar.consensus.fasta 28676 226.696 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-nextclade_one_sample/hCoV-19_USA_TX-DSHS-2263_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-stats_n_coverage/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-stats_n_coverage/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.stats.txt 21419 21419 21419 35473 35473 35473 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-variant_call/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-variant_call/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0.03 0.02 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-read_QC_trim/read_QC_trim/1463f8d6-4e2f-482a-af35-128e325d740d/call-kraken2_raw/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-read_QC_trim/read_QC_trim/1463f8d6-4e2f-482a-af35-128e325d740d/call-kraken2_dehosted/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021_kraken2_report.txt 98.62 98.62 Kraken version 2.0.8-beta 38.4 60 NA E:L73F,N:T205I,ORF1a:T265I,ORF1a:I2227T,ORF1a:S3158T,ORF1b:P314L,ORF1b:P976L,ORF1b:D1183Y,ORF1b:M1197I,ORF3a:Q57H,S:S13I,S:W152C,S:L452R,S:D614G,S:E1195G 21C (Epsilon) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-nextclade_one_sample/hCoV-19_USA_TX-DSHS-2263_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-nextclade_one_sample/hCoV-19_USA_TX-DSHS-2263_2021.ivar.consensus.nextclade.tsv 1.9.0 0 1106 29782 B.1.427 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-pangolin3/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 12; Ref alleles 0; Amb alleles 1; Usher placements: B.1.427(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 95.9 V3_nCoV-2019.primer.bed 32.84 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-read_QC_trim/read_QC_trim/1463f8d6-4e2f-482a-af35-128e325d740d/call-bbduk/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-read_QC_trim/read_QC_trim/1463f8d6-4e2f-482a-af35-128e325d740d/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-read_QC_trim/read_QC_trim/1463f8d6-4e2f-482a-af35-128e325d740d/call-bbduk/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-read_QC_trim/read_QC_trim/1463f8d6-4e2f-482a-af35-128e325d740d/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_TX-DSHS-2263_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_TX-DSHS-2263_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-vadr/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.ivar.consensus/hCoV-19_USA_TX-DSHS-2263_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_USA_TX-UTA-000313_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-primer_trim/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-primer_trim/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-consensus/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.ivar.consensus.fasta 29779 2324.9 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-nextclade_one_sample/hCoV-19_USA_TX-UTA-000313_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-stats_n_coverage/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-stats_n_coverage/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.stats.txt 159592 159592 159592 222498 222498 222498 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-variant_call/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-variant_call/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0.2 0.15 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-read_QC_trim/read_QC_trim/6a9b8a50-069f-48c1-9af7-863dff238f80/call-kraken2_raw/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-read_QC_trim/read_QC_trim/6a9b8a50-069f-48c1-9af7-863dff238f80/call-kraken2_dehosted/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021_kraken2_report.txt 89.95 89.95 Kraken version 2.0.8-beta 38.6 60 ORF1a:S3675-,ORF1a:G3676-,ORF1a:F3677- N:P199L,N:M234I,N:A419P,ORF1a:T265I,ORF1a:L3201P,ORF1b:K82R,ORF1b:P314L,ORF1b:Q1011H,ORF3a:P42L,ORF3a:Q57H,ORF8:T11I,S:L5F,S:T95I,S:D253G,S:E484K,S:D614G,S:A701V 21F (Iota) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-nextclade_one_sample/hCoV-19_USA_TX-UTA-000313_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-nextclade_one_sample/hCoV-19_USA_TX-UTA-000313_2021.ivar.consensus.nextclade.tsv 1.9.0 0 57 29836 B.1.526 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-pangolin3/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 19; Ref alleles 4; Amb alleles 0; Usher placements: B.1.526(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.59 V3_nCoV-2019.primer.bed 97.18 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-read_QC_trim/read_QC_trim/6a9b8a50-069f-48c1-9af7-863dff238f80/call-bbduk/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-read_QC_trim/read_QC_trim/6a9b8a50-069f-48c1-9af7-863dff238f80/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-read_QC_trim/read_QC_trim/6a9b8a50-069f-48c1-9af7-863dff238f80/call-bbduk/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-read_QC_trim/read_QC_trim/6a9b8a50-069f-48c1-9af7-863dff238f80/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_TX-UTA-000313_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_TX-UTA-000313_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-vadr/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.ivar.consensus/hCoV-19_USA_TX-UTA-000313_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_Wales_PHWC-4C8F5E_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-primer_trim/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-primer_trim/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-consensus/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.ivar.consensus.fasta 29297 605.267 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-nextclade_one_sample/hCoV-19_Wales_PHWC-4C8F5E_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-stats_n_coverage/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-stats_n_coverage/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.stats.txt 75087 75087 75087 155158 154566 Uneven pairs: R1=155158, R2=154566 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-variant_call/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-variant_call/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-read_QC_trim/read_QC_trim/b9877e57-7da6-4766-bbde-e025f7e819aa/call-kraken2_raw/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-read_QC_trim/read_QC_trim/b9877e57-7da6-4766-bbde-e025f7e819aa/call-kraken2_dehosted/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021_kraken2_report.txt 99.84 99.84 Kraken version 2.0.8-beta 35.4 60 ORF1a:S3675-,ORF1a:G3676-,ORF1a:F3677-,S:H69-,S:V70-,S:Y144- N:D3L,N:R203K,N:G204R,N:S235F,ORF1a:T1001I,ORF1a:A1708D,ORF1a:I2230T,ORF1a:F2780L,ORF1b:P314L,ORF1b:K1383R,ORF1b:E1977D,ORF3a:L15F,ORF8:Q27*,ORF8:R52I,ORF8:Y73C,S:N501Y,S:A570D,S:D614G,S:P681H,S:T716I,S:S982A,S:D1118H 20I (Alpha, V1) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-nextclade_one_sample/hCoV-19_Wales_PHWC-4C8F5E_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-nextclade_one_sample/hCoV-19_Wales_PHWC-4C8F5E_2021.ivar.consensus.nextclade.tsv 1.9.0 0 482 29779 B.1.1.7 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-pangolin3/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 22; Ref alleles 1; Amb alleles 0; Usher placements: B.1.1.7(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 97.97 V3_nCoV-2019.primer.bed 22.56 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-read_QC_trim/read_QC_trim/b9877e57-7da6-4766-bbde-e025f7e819aa/call-bbduk/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-read_QC_trim/read_QC_trim/b9877e57-7da6-4766-bbde-e025f7e819aa/call-ncbi_scrub_pe/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-read_QC_trim/read_QC_trim/b9877e57-7da6-4766-bbde-e025f7e819aa/call-bbduk/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-read_QC_trim/read_QC_trim/b9877e57-7da6-4766-bbde-e025f7e819aa/call-ncbi_scrub_pe/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_Wales_PHWC-4C8F5E_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_Wales_PHWC-4C8F5E_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-vadr/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.ivar.consensus/hCoV-19_Wales_PHWC-4C8F5E_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 diff --git a/reference_files/CDC_VOI_VOC_Lineages_v1-5-3.tsv b/reference_files/CDC_VOI_VOC_Lineages_v1-5-3.tsv new file mode 100644 index 0000000..be4c31c --- /dev/null +++ b/reference_files/CDC_VOI_VOC_Lineages_v1-5-3.tsv @@ -0,0 +1,17 @@ +entity:CDC_VOI_VOC_Lineages_v1-5-3_id aligned_bai aligned_bam assembly_fasta assembly_length_unambiguous assembly_mean_coverage assembly_method auspice_json bbduk_docker bwa_version consensus_flagstat consensus_stats fastqc_clean1 fastqc_clean2 fastqc_clean_pairs fastqc_raw1 fastqc_raw2 fastqc_raw_pairs fastqc_version ivar_tsv ivar_variant_version ivar_vcf ivar_version_consensus ivar_version_primtrim kraken_human kraken_human_dehosted kraken_report kraken_report_dehosted kraken_sc2 kraken_sc2_dehosted kraken_version meanbaseq_trim meanmapq_trim nextclade_aa_dels nextclade_aa_subs nextclade_clade nextclade_json nextclade_tsv nextclade_version number_Degenerate number_N number_Total pango_lineage pango_lineage_report pangolin_assignment_version pangolin_conflicts pangolin_docker pangolin_notes pangolin_versions percent_reference_coverage primer_bed_name primer_trimmed_read_percent read1_clean read1_dehosted read2_clean read2_dehosted read_1 read_2 samtools_version samtools_version_consensus samtools_version_primtrim samtools_version_stats seq_platform titan_illumina_pe_analysis_date titan_illumina_pe_version trimmomatic_version vadr_alerts_list vadr_docker vadr_num_alerts +hCoV-19_England_CAMC-13E7537_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-consensus/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.ivar.consensus.fasta 29287 1714.52 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-nextclade_one_sample/hCoV-19_England_CAMC-13E7537_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.stats.txt 163069 163069 163069 217320 216830 Uneven pairs: R1=217320, R2=216830 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-variant_call/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-variant_call/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-read_QC_trim/read_QC_trim/340aef6d-c5ee-4257-a3a2-cf5eaf5c4e16/call-kraken2_raw/cacheCopy/hCoV-19_England_CAMC-13E7537_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-read_QC_trim/read_QC_trim/340aef6d-c5ee-4257-a3a2-cf5eaf5c4e16/call-kraken2_dehosted/cacheCopy/hCoV-19_England_CAMC-13E7537_2021_kraken2_report.txt 99.66 99.66 Kraken version 2.0.8-beta 36.4 60 ORF1a:S3675-,ORF1a:G3676-,ORF1a:F3677- N:P80R,N:R203K,N:G204R,N:D348H,ORF1a:S1188L,ORF1a:K1795Q,ORF1a:D3526N,ORF1b:P314L,ORF1b:E1264D,ORF3a:S253P,ORF8:E92K,ORF9b:Q77E,S:L18F,S:T20N,S:P26S,S:D138Y,S:R190S,S:K417T,S:E484K,S:N501Y,S:D614G,S:H655Y,S:T1027I 20J (Gamma, V3) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-nextclade_one_sample/hCoV-19_England_CAMC-13E7537_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-nextclade_one_sample/hCoV-19_England_CAMC-13E7537_2021.ivar.consensus.nextclade.tsv 1.9.0 0 515 29802 P.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-pangolin3/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 14; Ref alleles 0; Amb alleles 0; Usher placements: P.1(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 97.94 V3_nCoV-2019.primer.bed 99.01 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-read_QC_trim/read_QC_trim/340aef6d-c5ee-4257-a3a2-cf5eaf5c4e16/call-bbduk/cacheCopy/hCoV-19_England_CAMC-13E7537_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-read_QC_trim/read_QC_trim/340aef6d-c5ee-4257-a3a2-cf5eaf5c4e16/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-13E7537_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-read_QC_trim/read_QC_trim/340aef6d-c5ee-4257-a3a2-cf5eaf5c4e16/call-bbduk/cacheCopy/hCoV-19_England_CAMC-13E7537_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-read_QC_trim/read_QC_trim/340aef6d-c5ee-4257-a3a2-cf5eaf5c4e16/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-13E7537_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-13E7537_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-13E7537_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fcdb37ee-3a5c-41ca-893b-963a65460332/call-vadr/cacheCopy/hCoV-19_England_CAMC-13E7537_2021.ivar.consensus/hCoV-19_England_CAMC-13E7537_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_England_CAMC-14E726C_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-consensus/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.ivar.consensus.fasta 29238 1167.1 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-nextclade_one_sample/hCoV-19_England_CAMC-14E726C_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.stats.txt 116979 116979 116979 198715 198332 Uneven pairs: R1=198715, R2=198332 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-variant_call/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-variant_call/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0.01 0.01 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-read_QC_trim/read_QC_trim/71f2f07a-75c3-4e91-b388-e1eafe9d6f8b/call-kraken2_raw/cacheCopy/hCoV-19_England_CAMC-14E726C_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-read_QC_trim/read_QC_trim/71f2f07a-75c3-4e91-b388-e1eafe9d6f8b/call-kraken2_dehosted/cacheCopy/hCoV-19_England_CAMC-14E726C_2021_kraken2_report.txt 79.23 79.23 Kraken version 2.0.8-beta 36.4 60 NA M:I82S,N:R203M,N:D377Y,ORF1a:T1241I,ORF1a:T1567I,ORF1a:T3646A,ORF1b:P314L,ORF1b:G1129C,ORF1b:M1352I,ORF1b:M1581I,ORF1b:K2310R,ORF1b:S2312A,ORF3a:S26L,ORF7a:V82A,S:T95I,S:G142D,S:E154K,S:L452R,S:E484Q,S:D614G,S:P681R,S:Q1071H 21B (Kappa) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-nextclade_one_sample/hCoV-19_England_CAMC-14E726C_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-nextclade_one_sample/hCoV-19_England_CAMC-14E726C_2021.ivar.consensus.nextclade.tsv 1.9.0 0 567 29805 B.1.617.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-pangolin3/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 11; Ref alleles 0; Amb alleles 0; Usher placements: B.1.617.1(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 97.78 V3_nCoV-2019.primer.bed 99.4 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-read_QC_trim/read_QC_trim/71f2f07a-75c3-4e91-b388-e1eafe9d6f8b/call-bbduk/cacheCopy/hCoV-19_England_CAMC-14E726C_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-read_QC_trim/read_QC_trim/71f2f07a-75c3-4e91-b388-e1eafe9d6f8b/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-14E726C_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-read_QC_trim/read_QC_trim/71f2f07a-75c3-4e91-b388-e1eafe9d6f8b/call-bbduk/cacheCopy/hCoV-19_England_CAMC-14E726C_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-read_QC_trim/read_QC_trim/71f2f07a-75c3-4e91-b388-e1eafe9d6f8b/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-14E726C_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-14E726C_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-14E726C_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f5dbfb02-32bb-4604-b669-3d65ce5993b4/call-vadr/cacheCopy/hCoV-19_England_CAMC-14E726C_2021.ivar.consensus/hCoV-19_England_CAMC-14E726C_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_England_CAMC-14E7A0A_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-consensus/hCoV-19_England_CAMC-14E7A0A_2021.ivar.consensus.fasta 29794 15954.5 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-nextclade_one_sample/hCoV-19_England_CAMC-14E7A0A_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021.stats.txt 1478767 1478767 1478767 1893395 1890185 Uneven pairs: R1=1893395, R2=1890185 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-variant_call/hCoV-19_England_CAMC-14E7A0A_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-variant_call/hCoV-19_England_CAMC-14E7A0A_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-read_QC_trim/read_QC_trim/aa3dd91d-b30f-4ae6-abb4-aac1fddda110/call-kraken2_raw/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-read_QC_trim/read_QC_trim/aa3dd91d-b30f-4ae6-abb4-aac1fddda110/call-kraken2_dehosted/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021_kraken2_report.txt 100 100 Kraken version 2.0.8-beta 36.4 60 ORF8:D119-,ORF8:F120-,S:E156-,S:F157- M:I82T,N:D63G,N:R203M,N:G215C,N:D377Y,ORF1a:A1306S,ORF1a:P2046L,ORF1a:P2287S,ORF1a:V2930L,ORF1a:T3255I,ORF1a:T3646A,ORF1b:P314L,ORF1b:G662S,ORF1b:P1000L,ORF1b:A1918V,ORF3a:S26L,ORF7a:V82A,ORF7a:T120I,ORF7b:T40I,ORF9b:T60A,S:T19R,S:G142D,S:R158G,S:L452R,S:T478K,S:D614G,S:P681R,S:D950N 21J (Delta) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-nextclade_one_sample/hCoV-19_England_CAMC-14E7A0A_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-nextclade_one_sample/hCoV-19_England_CAMC-14E7A0A_2021.ivar.consensus.nextclade.tsv 1.9.0 0 58 29852 B.1.617.2 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-pangolin3/hCoV-19_England_CAMC-14E7A0A_2021.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.64 V3_nCoV-2019.primer.bed 99.9 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-read_QC_trim/read_QC_trim/aa3dd91d-b30f-4ae6-abb4-aac1fddda110/call-bbduk/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-read_QC_trim/read_QC_trim/aa3dd91d-b30f-4ae6-abb4-aac1fddda110/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-read_QC_trim/read_QC_trim/aa3dd91d-b30f-4ae6-abb4-aac1fddda110/call-bbduk/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-read_QC_trim/read_QC_trim/aa3dd91d-b30f-4ae6-abb4-aac1fddda110/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-14E7A0A_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-14E7A0A_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-14E7A0A_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/c571e08e-44bb-4cd9-8198-4a9412aa79df/call-vadr/hCoV-19_England_CAMC-14E7A0A_2021.ivar.consensus/hCoV-19_England_CAMC-14E7A0A_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_England_CAMC-1510779_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-1510779_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-primer_trim/cacheCopy/hCoV-19_England_CAMC-1510779_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-consensus/cacheCopy/hCoV-19_England_CAMC-1510779_2021.ivar.consensus.fasta 29513 8814.18 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-nextclade_one_sample/hCoV-19_England_CAMC-1510779_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-1510779_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-stats_n_coverage/cacheCopy/hCoV-19_England_CAMC-1510779_2021.stats.txt 849766 849766 849766 1113379 1111258 Uneven pairs: R1=1113379, R2=1111258 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-variant_call/cacheCopy/hCoV-19_England_CAMC-1510779_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-variant_call/cacheCopy/hCoV-19_England_CAMC-1510779_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-read_QC_trim/read_QC_trim/bf546401-91fc-4cba-b351-ffe98e11c894/call-kraken2_raw/cacheCopy/hCoV-19_England_CAMC-1510779_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-read_QC_trim/read_QC_trim/bf546401-91fc-4cba-b351-ffe98e11c894/call-kraken2_dehosted/cacheCopy/hCoV-19_England_CAMC-1510779_2021_kraken2_report.txt 99.99 99.99 Kraken version 2.0.8-beta 36.4 60 NA M:I82S,N:R203M,N:D377Y,ORF1a:T1567I,ORF1a:T3646A,ORF1b:T17I,ORF1b:P314L,ORF1b:G1129C,ORF1b:M1352I,ORF1b:K2310R,ORF1b:S2312A,ORF3a:S26L,ORF7a:V82A,S:T95I,S:G142D,S:E154K,S:L452R,S:E484Q,S:D614G,S:P681R,S:Q1071H 21B (Kappa) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-nextclade_one_sample/hCoV-19_England_CAMC-1510779_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-nextclade_one_sample/hCoV-19_England_CAMC-1510779_2021.ivar.consensus.nextclade.tsv 1.9.0 0 292 29805 B.1.617.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-pangolin3/cacheCopy/hCoV-19_England_CAMC-1510779_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 11; Ref alleles 0; Amb alleles 0; Usher placements: B.1.617.1(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 98.7 V3_nCoV-2019.primer.bed 99.88 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-read_QC_trim/read_QC_trim/bf546401-91fc-4cba-b351-ffe98e11c894/call-bbduk/cacheCopy/hCoV-19_England_CAMC-1510779_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-read_QC_trim/read_QC_trim/bf546401-91fc-4cba-b351-ffe98e11c894/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-1510779_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-read_QC_trim/read_QC_trim/bf546401-91fc-4cba-b351-ffe98e11c894/call-bbduk/cacheCopy/hCoV-19_England_CAMC-1510779_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-read_QC_trim/read_QC_trim/bf546401-91fc-4cba-b351-ffe98e11c894/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_CAMC-1510779_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-1510779_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_CAMC-1510779_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/23346a72-6d9f-422f-b3ee-2f58afbf1f34/call-vadr/cacheCopy/hCoV-19_England_CAMC-1510779_2021.ivar.consensus/hCoV-19_England_CAMC-1510779_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_England_QEUH-14A3615_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-primer_trim/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-primer_trim/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-consensus/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.ivar.consensus.fasta 29610 14008.5 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-nextclade_one_sample/hCoV-19_England_QEUH-14A3615_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-stats_n_coverage/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-stats_n_coverage/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.stats.txt 1303647 1303647 1303647 1738634 1735175 Uneven pairs: R1=1738634, R2=1735175 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-variant_call/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-variant_call/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-read_QC_trim/read_QC_trim/b1940cba-d064-4812-8677-2f9e852ac76f/call-kraken2_raw/cacheCopy/hCoV-19_England_QEUH-14A3615_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-read_QC_trim/read_QC_trim/b1940cba-d064-4812-8677-2f9e852ac76f/call-kraken2_dehosted/cacheCopy/hCoV-19_England_QEUH-14A3615_2021_kraken2_report.txt 100 100 Kraken version 2.0.8-beta 36.4 60 ORF1a:S3675-,ORF1a:G3676-,ORF1a:F3677-,S:L241-,S:L242-,S:A243- E:P71L,N:T205I,ORF1a:T265I,ORF1a:K1655N,ORF1a:T2069I,ORF1a:K3353R,ORF1b:P314L,ORF1b:T1511I,ORF3a:Q57H,ORF3a:S171L,ORF8:I121L,S:D80A,S:D215G,S:K417N,S:E484K,S:N501Y,S:D614G,S:A701V 20H (Beta, V2) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-nextclade_one_sample/hCoV-19_England_QEUH-14A3615_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-nextclade_one_sample/hCoV-19_England_QEUH-14A3615_2021.ivar.consensus.nextclade.tsv 1.9.0 0 234 29844 B.1.351 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-pangolin3/cacheCopy/hCoV-19_England_QEUH-14A3615_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 12; Ref alleles 0; Amb alleles 0; Usher placements: B.1.351(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.02 V3_nCoV-2019.primer.bed 99.84 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-read_QC_trim/read_QC_trim/b1940cba-d064-4812-8677-2f9e852ac76f/call-bbduk/cacheCopy/hCoV-19_England_QEUH-14A3615_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-read_QC_trim/read_QC_trim/b1940cba-d064-4812-8677-2f9e852ac76f/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_QEUH-14A3615_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-read_QC_trim/read_QC_trim/b1940cba-d064-4812-8677-2f9e852ac76f/call-bbduk/cacheCopy/hCoV-19_England_QEUH-14A3615_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-read_QC_trim/read_QC_trim/b1940cba-d064-4812-8677-2f9e852ac76f/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_QEUH-14A3615_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_QEUH-14A3615_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_QEUH-14A3615_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/1d851f71-6958-4cf8-8b59-bfd594df9c65/call-vadr/hCoV-19_England_QEUH-14A3615_2021.ivar.consensus/hCoV-19_England_QEUH-14A3615_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_England_QEUH-E93AAC_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-primer_trim/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-primer_trim/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-consensus/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.ivar.consensus.fasta 29733 8331.92 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-nextclade_one_sample/hCoV-19_England_QEUH-E93AAC_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-stats_n_coverage/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-stats_n_coverage/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.stats.txt 756413 756413 756413 915559 912627 Uneven pairs: R1=915559, R2=912627 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-variant_call/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-variant_call/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-read_QC_trim/read_QC_trim/69740b61-1a23-4c7b-bdf6-589abb6c01ac/call-kraken2_raw/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-read_QC_trim/read_QC_trim/69740b61-1a23-4c7b-bdf6-589abb6c01ac/call-kraken2_dehosted/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021_kraken2_report.txt 99.99 99.99 Kraken version 2.0.8-beta 36.5 60 N:M1-,ORF1a:S3675-,ORF1a:G3676-,ORF1a:F3677-,ORF6:M1-,S:H69-,S:V70-,S:Y144- E:L21F,M:I82T,N:S2M,N:D3Y,N:A12G,N:T205I,ORF1a:T2007I,ORF1b:P314F,ORF1b:D1735N,ORF6:F2M,ORF8:G8V,ORF9b:H9D,S:Q52R,S:A67V,S:E484K,S:D614G,S:Q677H,S:F888L 21D (Eta) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-nextclade_one_sample/hCoV-19_England_QEUH-E93AAC_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-nextclade_one_sample/hCoV-19_England_QEUH-E93AAC_2021.ivar.consensus.nextclade.tsv 1.9.0 0 0 29733 B.1.525 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-pangolin3/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.43 V3_nCoV-2019.primer.bed 99.89 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-read_QC_trim/read_QC_trim/69740b61-1a23-4c7b-bdf6-589abb6c01ac/call-bbduk/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-read_QC_trim/read_QC_trim/69740b61-1a23-4c7b-bdf6-589abb6c01ac/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-read_QC_trim/read_QC_trim/69740b61-1a23-4c7b-bdf6-589abb6c01ac/call-bbduk/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-read_QC_trim/read_QC_trim/69740b61-1a23-4c7b-bdf6-589abb6c01ac/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_QEUH-E93AAC_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_QEUH-E93AAC_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/0b02b2fc-8430-4792-a54f-a37b92807d4e/call-vadr/cacheCopy/hCoV-19_England_QEUH-E93AAC_2021.ivar.consensus/hCoV-19_England_QEUH-E93AAC_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_England_QEUH-E948CF_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-primer_trim/cacheCopy/hCoV-19_England_QEUH-E948CF_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-primer_trim/cacheCopy/hCoV-19_England_QEUH-E948CF_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-consensus/cacheCopy/hCoV-19_England_QEUH-E948CF_2021.ivar.consensus.fasta 29759 13302 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-nextclade_one_sample/hCoV-19_England_QEUH-E948CF_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-stats_n_coverage/cacheCopy/hCoV-19_England_QEUH-E948CF_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-stats_n_coverage/cacheCopy/hCoV-19_England_QEUH-E948CF_2021.stats.txt 1208467 1208467 1208467 1507565 1500580 Uneven pairs: R1=1507565, R2=1500580 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-variant_call/cacheCopy/hCoV-19_England_QEUH-E948CF_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-variant_call/cacheCopy/hCoV-19_England_QEUH-E948CF_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-read_QC_trim/read_QC_trim/0100ef85-42b9-46d4-80d1-be8fcd09672a/call-kraken2_raw/cacheCopy/hCoV-19_England_QEUH-E948CF_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-read_QC_trim/read_QC_trim/0100ef85-42b9-46d4-80d1-be8fcd09672a/call-kraken2_dehosted/cacheCopy/hCoV-19_England_QEUH-E948CF_2021_kraken2_report.txt 100 100 Kraken version 2.0.8-beta 36.5 60 N:M1-,ORF1a:S3675-,ORF1a:G3676-,ORF1a:F3677-,ORF6:M1-,S:H69-,S:V70-,S:Y144- E:L21F,M:I82T,N:S2M,N:D3Y,N:A12G,N:T205I,ORF1a:T2007I,ORF1b:P314F,ORF1b:D1735N,ORF6:F2M,ORF8:G8V,ORF9b:H9D,S:Q52R,S:A67V,S:E484K,S:D614G,S:Q677H,S:F888L 21D (Eta) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-nextclade_one_sample/hCoV-19_England_QEUH-E948CF_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-nextclade_one_sample/hCoV-19_England_QEUH-E948CF_2021.ivar.consensus.nextclade.tsv 1.9.0 0 33 29792 B.1.525 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-pangolin3/hCoV-19_England_QEUH-E948CF_2021.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.52 V3_nCoV-2019.primer.bed 99.88 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-read_QC_trim/read_QC_trim/0100ef85-42b9-46d4-80d1-be8fcd09672a/call-bbduk/cacheCopy/hCoV-19_England_QEUH-E948CF_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-read_QC_trim/read_QC_trim/0100ef85-42b9-46d4-80d1-be8fcd09672a/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_QEUH-E948CF_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-read_QC_trim/read_QC_trim/0100ef85-42b9-46d4-80d1-be8fcd09672a/call-bbduk/cacheCopy/hCoV-19_England_QEUH-E948CF_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-read_QC_trim/read_QC_trim/0100ef85-42b9-46d4-80d1-be8fcd09672a/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_QEUH-E948CF_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_QEUH-E948CF_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_QEUH-E948CF_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/fe55b145-abfb-4e13-b0fe-b66ff72444a3/call-vadr/hCoV-19_England_QEUH-E948CF_2021.ivar.consensus/hCoV-19_England_QEUH-E948CF_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_England_RAND-14DD366_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-primer_trim/cacheCopy/hCoV-19_England_RAND-14DD366_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-primer_trim/cacheCopy/hCoV-19_England_RAND-14DD366_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-consensus/hCoV-19_England_RAND-14DD366_2021.ivar.consensus.fasta 29806 19422.1 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-nextclade_one_sample/hCoV-19_England_RAND-14DD366_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-stats_n_coverage/cacheCopy/hCoV-19_England_RAND-14DD366_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-stats_n_coverage/cacheCopy/hCoV-19_England_RAND-14DD366_2021.stats.txt 1818270 1818270 1818270 2326577 2323879 Uneven pairs: R1=2326577, R2=2323879 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-variant_call/hCoV-19_England_RAND-14DD366_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-variant_call/hCoV-19_England_RAND-14DD366_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-read_QC_trim/read_QC_trim/1cd92919-9ea9-4360-b380-2f6f51b9d127/call-kraken2_raw/cacheCopy/hCoV-19_England_RAND-14DD366_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-read_QC_trim/read_QC_trim/1cd92919-9ea9-4360-b380-2f6f51b9d127/call-kraken2_dehosted/cacheCopy/hCoV-19_England_RAND-14DD366_2021_kraken2_report.txt 100 100 Kraken version 2.0.8-beta 36.4 60 ORF8:D119-,ORF8:F120-,S:E156-,S:F157- M:I82T,N:D63G,N:R203M,N:G215C,N:D377Y,ORF1a:A1306S,ORF1a:P2046L,ORF1a:P2287S,ORF1a:V2930L,ORF1a:T3255I,ORF1a:T3646A,ORF1b:P314L,ORF1b:G662S,ORF1b:P1000L,ORF1b:A1918V,ORF3a:S26L,ORF7a:V82A,ORF7a:T120I,ORF7b:T40I,ORF9b:T60A,S:T19R,S:G142D,S:R158G,S:L452R,S:T478K,S:D614G,S:P681R,S:D950N 21J (Delta) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-nextclade_one_sample/hCoV-19_England_RAND-14DD366_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-nextclade_one_sample/hCoV-19_England_RAND-14DD366_2021.ivar.consensus.nextclade.tsv 1.9.0 0 51 29857 B.1.617.2 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-pangolin3/hCoV-19_England_RAND-14DD366_2021.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.68 V3_nCoV-2019.primer.bed 99.82 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-read_QC_trim/read_QC_trim/1cd92919-9ea9-4360-b380-2f6f51b9d127/call-bbduk/cacheCopy/hCoV-19_England_RAND-14DD366_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-read_QC_trim/read_QC_trim/1cd92919-9ea9-4360-b380-2f6f51b9d127/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_RAND-14DD366_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-read_QC_trim/read_QC_trim/1cd92919-9ea9-4360-b380-2f6f51b9d127/call-bbduk/cacheCopy/hCoV-19_England_RAND-14DD366_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-read_QC_trim/read_QC_trim/1cd92919-9ea9-4360-b380-2f6f51b9d127/call-ncbi_scrub_pe/cacheCopy/hCoV-19_England_RAND-14DD366_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_RAND-14DD366_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_England_RAND-14DD366_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/6952a4b4-e8c4-43a7-8e30-ea21e14a916d/call-vadr/hCoV-19_England_RAND-14DD366_2021.ivar.consensus/hCoV-19_England_RAND-14DD366_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_USA_CA-QDX-2761_2020 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-primer_trim/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-primer_trim/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-consensus/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.ivar.consensus.fasta 29702 1242.74 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-nextclade_one_sample/hCoV-19_USA_CA-QDX-2761_2020.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-stats_n_coverage/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-stats_n_coverage/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.stats.txt 95702 95702 95702 146635 146635 146635 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-variant_call/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-variant_call/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0.2 0.07 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-read_QC_trim/read_QC_trim/c862bce2-093e-4cfe-be2a-754eed06ca72/call-kraken2_raw/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-read_QC_trim/read_QC_trim/c862bce2-093e-4cfe-be2a-754eed06ca72/call-kraken2_dehosted/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020_kraken2_report.txt 96.74 96.74 Kraken version 2.0.8-beta 37.6 60 NA N:T205I,ORF1a:R77L,ORF1a:T265I,ORF1a:S3158T,ORF1b:P314L,ORF1b:P976L,ORF1b:D1183Y,ORF3a:Q57H,S:S13I,S:W152C,S:L452R,S:D614G 21C (Epsilon) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-nextclade_one_sample/hCoV-19_USA_CA-QDX-2761_2020.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-nextclade_one_sample/hCoV-19_USA_CA-QDX-2761_2020.ivar.consensus.nextclade.tsv 1.9.0 0 104 29806 B.1.427 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-pangolin3/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.33 V3_nCoV-2019.primer.bed 96.08 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-read_QC_trim/read_QC_trim/c862bce2-093e-4cfe-be2a-754eed06ca72/call-bbduk/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-read_QC_trim/read_QC_trim/c862bce2-093e-4cfe-be2a-754eed06ca72/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-read_QC_trim/read_QC_trim/c862bce2-093e-4cfe-be2a-754eed06ca72/call-bbduk/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-read_QC_trim/read_QC_trim/c862bce2-093e-4cfe-be2a-754eed06ca72/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_CA-QDX-2761_2020_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_CA-QDX-2761_2020_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/62ccd8dc-47d9-4bc7-9153-9d58fe2f25b3/call-vadr/cacheCopy/hCoV-19_USA_CA-QDX-2761_2020.ivar.consensus/hCoV-19_USA_CA-QDX-2761_2020.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_USA_CA-QDX-2781_2020 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-primer_trim/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-primer_trim/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-consensus/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.ivar.consensus.fasta 29559 608.594 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-nextclade_one_sample/hCoV-19_USA_CA-QDX-2781_2020.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-stats_n_coverage/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-stats_n_coverage/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.stats.txt 47611 47611 47611 76082 76082 76082 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-variant_call/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-variant_call/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0.06 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-read_QC_trim/read_QC_trim/185061c1-fdaf-403b-87aa-1b9e8156b2e4/call-kraken2_raw/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-read_QC_trim/read_QC_trim/185061c1-fdaf-403b-87aa-1b9e8156b2e4/call-kraken2_dehosted/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020_kraken2_report.txt 97.38 97.38 Kraken version 2.0.8-beta 37.6 60 NA N:T205I,ORF1a:T265I,ORF1a:A1473V,ORF1a:H2125Y,ORF1a:V3595G,ORF1a:F3789L,ORF1a:C3790F,ORF1a:I4205V,ORF1b:P314L,ORF1b:D1183Y,ORF1b:T2537I,ORF3a:Q57H,S:S13I,S:W152C,S:L452R,S:D614G 21C (Epsilon) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-nextclade_one_sample/hCoV-19_USA_CA-QDX-2781_2020.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-nextclade_one_sample/hCoV-19_USA_CA-QDX-2781_2020.ivar.consensus.nextclade.tsv 1.9.0 0 265 29824 B.1.429 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-pangolin3/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 98.85 V3_nCoV-2019.primer.bed 96.58 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-read_QC_trim/read_QC_trim/185061c1-fdaf-403b-87aa-1b9e8156b2e4/call-bbduk/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-read_QC_trim/read_QC_trim/185061c1-fdaf-403b-87aa-1b9e8156b2e4/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-read_QC_trim/read_QC_trim/185061c1-fdaf-403b-87aa-1b9e8156b2e4/call-bbduk/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-read_QC_trim/read_QC_trim/185061c1-fdaf-403b-87aa-1b9e8156b2e4/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_CA-QDX-2781_2020_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_CA-QDX-2781_2020_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/d0550ebe-d52f-407a-b727-419a3191db7d/call-vadr/cacheCopy/hCoV-19_USA_CA-QDX-2781_2020.ivar.consensus/hCoV-19_USA_CA-QDX-2781_2020.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_USA_MA-QDX-2966_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-primer_trim/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-primer_trim/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-consensus/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.ivar.consensus.fasta 29807 802.693 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-nextclade_one_sample/hCoV-19_USA_MA-QDX-2966_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-stats_n_coverage/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-stats_n_coverage/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.stats.txt 56291 56291 56291 73899 73899 73899 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-variant_call/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-variant_call/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 1.9 0.53 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-read_QC_trim/read_QC_trim/2d8be66e-6d1c-4c75-b8be-f6ef4e5b3dfd/call-kraken2_raw/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-read_QC_trim/read_QC_trim/2d8be66e-6d1c-4c75-b8be-f6ef4e5b3dfd/call-kraken2_dehosted/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021_kraken2_report.txt 91.8 91.8 Kraken version 2.0.8-beta 37.8 60 NA N:A119S,N:R203K,N:G204R,N:M234I,ORF1a:L3468V,ORF1a:L3930F,ORF1b:P314L,ORF1b:T2432I,S:E484K,S:D614G,S:V1176F 20B gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-nextclade_one_sample/hCoV-19_USA_MA-QDX-2966_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-nextclade_one_sample/hCoV-19_USA_MA-QDX-2966_2021.ivar.consensus.nextclade.tsv 1.9.0 0 26 29833 P.2 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-pangolin3/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.68 V3_nCoV-2019.primer.bed 95.72 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-read_QC_trim/read_QC_trim/2d8be66e-6d1c-4c75-b8be-f6ef4e5b3dfd/call-bbduk/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-read_QC_trim/read_QC_trim/2d8be66e-6d1c-4c75-b8be-f6ef4e5b3dfd/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-read_QC_trim/read_QC_trim/2d8be66e-6d1c-4c75-b8be-f6ef4e5b3dfd/call-bbduk/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-read_QC_trim/read_QC_trim/2d8be66e-6d1c-4c75-b8be-f6ef4e5b3dfd/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_MA-QDX-2966_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_MA-QDX-2966_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/f1e6fa82-7182-454a-a969-80e6629479b2/call-vadr/cacheCopy/hCoV-19_USA_MA-QDX-2966_2021.ivar.consensus/hCoV-19_USA_MA-QDX-2966_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_USA_NV-QDX-4024_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-primer_trim/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-primer_trim/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-consensus/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.ivar.consensus.fasta 29806 972.978 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-nextclade_one_sample/hCoV-19_USA_NV-QDX-4024_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-stats_n_coverage/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-stats_n_coverage/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.stats.txt 69643 69643 69643 92107 92107 92107 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-variant_call/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-variant_call/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0.07 0.02 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-read_QC_trim/read_QC_trim/f959c14e-c07f-46ce-9a99-ab03cac6e55f/call-kraken2_raw/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-read_QC_trim/read_QC_trim/f959c14e-c07f-46ce-9a99-ab03cac6e55f/call-kraken2_dehosted/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021_kraken2_report.txt 95.28 95.28 Kraken version 2.0.8-beta 37.7 60 NA N:A119S,N:R203K,N:G204R,N:M234I,ORF1a:L3468V,ORF1a:L3930F,ORF1a:T4249I,ORF1b:P314L,S:E484K,S:D614G,S:V1176F 20B gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-nextclade_one_sample/hCoV-19_USA_NV-QDX-4024_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-nextclade_one_sample/hCoV-19_USA_NV-QDX-4024_2021.ivar.consensus.nextclade.tsv 1.9.0 0 18 29824 P.2 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-pangolin3/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.pangolin_report.csv pangolin 3.1.17; PANGO-v1.2.121 staphb/pangolin:3.1.17-pangolearn-2022-01-05 Assigned from designation hash. pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.68 V3_nCoV-2019.primer.bed 96.98 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-read_QC_trim/read_QC_trim/f959c14e-c07f-46ce-9a99-ab03cac6e55f/call-bbduk/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-read_QC_trim/read_QC_trim/f959c14e-c07f-46ce-9a99-ab03cac6e55f/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-read_QC_trim/read_QC_trim/f959c14e-c07f-46ce-9a99-ab03cac6e55f/call-bbduk/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-read_QC_trim/read_QC_trim/f959c14e-c07f-46ce-9a99-ab03cac6e55f/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_NV-QDX-4024_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_NV-QDX-4024_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/efdc847c-49d4-4d8e-a078-88503f30c9dd/call-vadr/cacheCopy/hCoV-19_USA_NV-QDX-4024_2021.ivar.consensus/hCoV-19_USA_NV-QDX-4024_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_USA_RI-QDX-3232_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-primer_trim/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-primer_trim/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-consensus/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.ivar.consensus.fasta 29796 1091.8 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-nextclade_one_sample/hCoV-19_USA_RI-QDX-3232_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-stats_n_coverage/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-stats_n_coverage/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.stats.txt 82348 82348 82348 102908 102908 102908 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-variant_call/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-variant_call/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0.01 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-read_QC_trim/read_QC_trim/1265ab8d-f615-43af-93ed-f50ab52d507d/call-kraken2_raw/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-read_QC_trim/read_QC_trim/1265ab8d-f615-43af-93ed-f50ab52d507d/call-kraken2_dehosted/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021_kraken2_report.txt 97.04 97.04 Kraken version 2.0.8-beta 37.6 60 ORF1a:S3675-,ORF1a:G3676-,ORF1a:F3677- N:P199L,N:M234I,ORF1a:T265I,ORF1a:L3201P,ORF1b:P314L,ORF1b:Q813H,ORF1b:Q1011H,ORF3a:P42L,ORF3a:Q57H,ORF8:T11I,S:L5F,S:T95I,S:D253G,S:E484K,S:D614G,S:A701V 21F (Iota) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-nextclade_one_sample/hCoV-19_USA_RI-QDX-3232_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-nextclade_one_sample/hCoV-19_USA_RI-QDX-3232_2021.ivar.consensus.nextclade.tsv 1.9.0 0 28 29824 B.1.526 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-pangolin3/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 19; Ref alleles 4; Amb alleles 0; Usher placements: B.1.526(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.64 V3_nCoV-2019.primer.bed 96.75 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-read_QC_trim/read_QC_trim/1265ab8d-f615-43af-93ed-f50ab52d507d/call-bbduk/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-read_QC_trim/read_QC_trim/1265ab8d-f615-43af-93ed-f50ab52d507d/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-read_QC_trim/read_QC_trim/1265ab8d-f615-43af-93ed-f50ab52d507d/call-bbduk/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-read_QC_trim/read_QC_trim/1265ab8d-f615-43af-93ed-f50ab52d507d/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_RI-QDX-3232_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_RI-QDX-3232_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/a87b1001-9da2-45cb-8b74-f6e4189228cc/call-vadr/cacheCopy/hCoV-19_USA_RI-QDX-3232_2021.ivar.consensus/hCoV-19_USA_RI-QDX-3232_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_USA_TX-DSHS-2263_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-primer_trim/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-primer_trim/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-consensus/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.ivar.consensus.fasta 28676 226.696 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-nextclade_one_sample/hCoV-19_USA_TX-DSHS-2263_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-stats_n_coverage/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-stats_n_coverage/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.stats.txt 21419 21419 21419 35473 35473 35473 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-variant_call/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-variant_call/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0.03 0.02 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-read_QC_trim/read_QC_trim/1463f8d6-4e2f-482a-af35-128e325d740d/call-kraken2_raw/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-read_QC_trim/read_QC_trim/1463f8d6-4e2f-482a-af35-128e325d740d/call-kraken2_dehosted/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021_kraken2_report.txt 98.62 98.62 Kraken version 2.0.8-beta 38.4 60 NA E:L73F,N:T205I,ORF1a:T265I,ORF1a:I2227T,ORF1a:S3158T,ORF1b:P314L,ORF1b:P976L,ORF1b:D1183Y,ORF1b:M1197I,ORF3a:Q57H,S:S13I,S:W152C,S:L452R,S:D614G,S:E1195G 21C (Epsilon) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-nextclade_one_sample/hCoV-19_USA_TX-DSHS-2263_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-nextclade_one_sample/hCoV-19_USA_TX-DSHS-2263_2021.ivar.consensus.nextclade.tsv 1.9.0 0 1106 29782 B.1.427 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-pangolin3/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 12; Ref alleles 0; Amb alleles 1; Usher placements: B.1.427(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 95.9 V3_nCoV-2019.primer.bed 32.84 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-read_QC_trim/read_QC_trim/1463f8d6-4e2f-482a-af35-128e325d740d/call-bbduk/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-read_QC_trim/read_QC_trim/1463f8d6-4e2f-482a-af35-128e325d740d/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-read_QC_trim/read_QC_trim/1463f8d6-4e2f-482a-af35-128e325d740d/call-bbduk/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-read_QC_trim/read_QC_trim/1463f8d6-4e2f-482a-af35-128e325d740d/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_TX-DSHS-2263_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_TX-DSHS-2263_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/3b6807c2-3870-4e35-9d19-3c236f5a68d1/call-vadr/cacheCopy/hCoV-19_USA_TX-DSHS-2263_2021.ivar.consensus/hCoV-19_USA_TX-DSHS-2263_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_USA_TX-UTA-000313_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-primer_trim/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-primer_trim/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-consensus/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.ivar.consensus.fasta 29779 2324.9 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-nextclade_one_sample/hCoV-19_USA_TX-UTA-000313_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-stats_n_coverage/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-stats_n_coverage/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.stats.txt 159592 159592 159592 222498 222498 222498 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-variant_call/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-variant_call/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0.2 0.15 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-read_QC_trim/read_QC_trim/6a9b8a50-069f-48c1-9af7-863dff238f80/call-kraken2_raw/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-read_QC_trim/read_QC_trim/6a9b8a50-069f-48c1-9af7-863dff238f80/call-kraken2_dehosted/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021_kraken2_report.txt 89.95 89.95 Kraken version 2.0.8-beta 38.6 60 ORF1a:S3675-,ORF1a:G3676-,ORF1a:F3677- N:P199L,N:M234I,N:A419P,ORF1a:T265I,ORF1a:L3201P,ORF1b:K82R,ORF1b:P314L,ORF1b:Q1011H,ORF3a:P42L,ORF3a:Q57H,ORF8:T11I,S:L5F,S:T95I,S:D253G,S:E484K,S:D614G,S:A701V 21F (Iota) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-nextclade_one_sample/hCoV-19_USA_TX-UTA-000313_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-nextclade_one_sample/hCoV-19_USA_TX-UTA-000313_2021.ivar.consensus.nextclade.tsv 1.9.0 0 57 29836 B.1.526 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-pangolin3/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 19; Ref alleles 4; Amb alleles 0; Usher placements: B.1.526(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 99.59 V3_nCoV-2019.primer.bed 97.18 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-read_QC_trim/read_QC_trim/6a9b8a50-069f-48c1-9af7-863dff238f80/call-bbduk/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-read_QC_trim/read_QC_trim/6a9b8a50-069f-48c1-9af7-863dff238f80/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-read_QC_trim/read_QC_trim/6a9b8a50-069f-48c1-9af7-863dff238f80/call-bbduk/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-read_QC_trim/read_QC_trim/6a9b8a50-069f-48c1-9af7-863dff238f80/call-ncbi_scrub_pe/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_TX-UTA-000313_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_USA_TX-UTA-000313_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/349fa4be-7a18-44c4-8434-277e5a1bcebb/call-vadr/cacheCopy/hCoV-19_USA_TX-UTA-000313_2021.ivar.consensus/hCoV-19_USA_TX-UTA-000313_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 +hCoV-19_Wales_PHWC-4C8F5E_2021 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-primer_trim/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.primertrim.sorted.bam.bai gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-primer_trim/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.primertrim.sorted.bam gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-consensus/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.ivar.consensus.fasta 29297 605.267 BWA Version: 0.7.17-r1188; iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-nextclade_one_sample/hCoV-19_Wales_PHWC-4C8F5E_2021.ivar.consensus.nextclade.auspice.json staphb/bbtools:38.76 BWA Version: 0.7.17-r1188 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-stats_n_coverage/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.flagstat.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-stats_n_coverage/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.stats.txt 75087 75087 75087 155158 154566 Uneven pairs: R1=155158, R2=154566 FastQC v0.11.8 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-variant_call/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.variants.tsv iVar version 1.3.1 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-variant_call/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.variants.vcf iVar version 1.3.1 iVar version 1.3.1 0 0 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-read_QC_trim/read_QC_trim/b9877e57-7da6-4766-bbde-e025f7e819aa/call-kraken2_raw/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021_kraken2_report.txt gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-read_QC_trim/read_QC_trim/b9877e57-7da6-4766-bbde-e025f7e819aa/call-kraken2_dehosted/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021_kraken2_report.txt 99.84 99.84 Kraken version 2.0.8-beta 35.4 60 ORF1a:S3675-,ORF1a:G3676-,ORF1a:F3677-,S:H69-,S:V70-,S:Y144- N:D3L,N:R203K,N:G204R,N:S235F,ORF1a:T1001I,ORF1a:A1708D,ORF1a:I2230T,ORF1a:F2780L,ORF1b:P314L,ORF1b:K1383R,ORF1b:E1977D,ORF3a:L15F,ORF8:Q27*,ORF8:R52I,ORF8:Y73C,S:N501Y,S:A570D,S:D614G,S:P681H,S:T716I,S:S982A,S:D1118H 20I (Alpha, V1) gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-nextclade_one_sample/hCoV-19_Wales_PHWC-4C8F5E_2021.ivar.consensus.nextclade.json gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-nextclade_one_sample/hCoV-19_Wales_PHWC-4C8F5E_2021.ivar.consensus.nextclade.tsv 1.9.0 0 482 29779 B.1.1.7 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-pangolin3/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.pangolin_report.csv pangolin 3.1.17; PUSHER-v1.2.121 0.0 staphb/pangolin:3.1.17-pangolearn-2022-01-05 scorpio call: Alt alleles 22; Ref alleles 1; Amb alleles 0; Usher placements: B.1.1.7(1/1) pangolin: 3.1.17;pangolearn: 2022-01-05;constellations: v0.1.1;scorpio: 0.3.16;pango-designation used by pangoLEARN/Usher: v1.2.121;pango-designation aliases: 1.2.122 97.97 V3_nCoV-2019.primer.bed 22.56 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-read_QC_trim/read_QC_trim/b9877e57-7da6-4766-bbde-e025f7e819aa/call-bbduk/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021_1.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-read_QC_trim/read_QC_trim/b9877e57-7da6-4766-bbde-e025f7e819aa/call-ncbi_scrub_pe/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021_R1_dehosted.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-read_QC_trim/read_QC_trim/b9877e57-7da6-4766-bbde-e025f7e819aa/call-bbduk/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021_2.clean.fastq.gz gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-read_QC_trim/read_QC_trim/b9877e57-7da6-4766-bbde-e025f7e819aa/call-ncbi_scrub_pe/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021_R2_dehosted.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_Wales_PHWC-4C8F5E_2021_1.fastq.gz gs://sc2_validation_data/cdc_voi_voc_lineages/hCoV-19_Wales_PHWC-4C8F5E_2021_2.fastq.gz samtools 1.12 samtools 1.12 samtools 1.12 samtools 1.10 Illumina paired-end 2022-01-19 PHVG v1.5.3 Trimmomatic 0.39 gs://fc-16050f07-6ecb-4e0e-b096-b9622e7c6397/16f38eab-14cb-4aab-b7fa-f0c8c3929686/titan_illumina_pe/4bb7c885-6e8e-42cf-8324-02569547c698/call-vadr/cacheCopy/hCoV-19_Wales_PHWC-4C8F5E_2021.ivar.consensus/hCoV-19_Wales_PHWC-4C8F5E_2021.ivar.consensus.vadr.alt.list staphb/vadr:1.3 0 diff --git a/scripts/compare-data-tables.py b/scripts/compare-data-tables.py new file mode 100755 index 0000000..f392499 --- /dev/null +++ b/scripts/compare-data-tables.py @@ -0,0 +1,141 @@ +#!/usr/bin/env python3 +""" +usage: compare-data-tables.py [-h] [--outdir STRING] [--prefix STRING] TSV TSV + +Compare two TSV files and report the differences + +positional arguments: + TSV The first TSV to compare. + TSV The second TSV file to compare + +options: + -h, --help show this help message and exit + --outdir STRING The directory to output files to. (Default: ./) + --prefix STRING The prefix to use for output files (Default: comparison) +""" +import pandas as pd + +def read_tsv(tsv_file): + """Read TSV and change first column to 'samples'""" + df = pd.read_csv(tsv_file, sep='\t').fillna('') + c1_name = df.columns.values[0] + df.columns.values[0] = "samples" + + return [df, c1_name] + +def write_html(data, html_out): + """Data to write to HTML""" + return None + +if __name__ == '__main__': + import argparse as ap + import os + import sys + import pdfkit as pdf + + parser = ap.ArgumentParser( + prog='compare-data-tables.py', + conflict_handler='resolve', + description=("Compare two TSV files and report the differences") + ) + parser.add_argument('tsv1', metavar="TSV", type=str, + help='The first TSV to compare.') + parser.add_argument('tsv2', metavar="TSV", type=str, + help='The second TSV file to compare') + parser.add_argument('--outdir', metavar="STRING", type=str, default='./', + help='The directory to output files to. (Default: ./)') + parser.add_argument('--prefix', metavar="STRING", type=str, default='comparison', + help='The prefix to use for output files (Default: comparison)') + + if len(sys.argv) == 1: + parser.print_help() + sys.exit(0) + + args = parser.parse_args() + + # Verify input exists + has_error = False + for tsv_file in [args.tsv1, args.tsv2]: + if not os.path.isfile(tsv_file): + print(f'Unable to locate TSV file: {tsv_file}', file=sys.stderr) + has_error = True + + if has_error: + sys.exit(1) + + # Read in TSVs + df1, df1_c1_name = read_tsv(args.tsv1) + df2, df2_c1_name = read_tsv(args.tsv2) + + print(df1.columns) + # Drop columns that will almost always differ, keep only the columns that matter for validating the workflow + keepers_list=['assembly_length_unambiguous','assembly_mean_coverage','assembly_method','kraken_human','kraken_human_dehosted','kraken_sc2','kraken_sc2_dehosted','meanbaseq_trim','meanmapq_trim','nextclade_aa_dels','nextclade_aa_subs','nextclade_clade','number_Degenerate','number_N','number_Total','pango_lineage','pangolin_conflicts','pangolin_notes','percent_reference_coverage','primer_bed_name','seq_platform','vadr_num_alerts','validation_set','primer_trimmed_read_percent'] + drop_list1 = [] + drop_list2 = [] + + for i in df1.columns: + if i not in keepers_list: + drop_list1.append(i) + df1.drop(drop_list1, axis='columns', inplace=True) + + for j in df2.columns: + if j not in keepers_list: + drop_list2.append(j) + df2.drop(drop_list2, axis='columns', inplace=True) + + if drop_list1 != drop_list2: + print('Datatables have different sets of extraneous columns.') + else: + print('Datatables have the same set of extraneous columns.') + + # Perform comparison + df_comp1 = df1.compare(df2, align_axis=1, keep_shape=True, keep_equal=False) + # Count non-NA values in each columns + val_cnts = df_comp1.count() + df_val_cnts=val_cnts.to_frame() + df_val_cnts.columns = ['Number of Diffs'] + print(df_val_cnts) + # Replace NAs with "EXACT_MATCH" + df_comp1.fillna(value='EXACT_MATCH', method=None, axis=None, inplace=True, limit=None, downcast=None) + + # Get the side-by-side comparison of the TSVs + # df_diff_vert = df1.compare(df2, align_axis = 0, keep_shape=True, keep_equal=True).transpose() + # df_comp_bool = df1.where() + #missing_samples = [] + + # Compare samples + #print(df1.samples.values) + #print('column\tis_same\ttsv1\ttsv2') + #print(f'filename\t{args.tsv1==args.tsv2}\t{args.tsv1}\t{args.tsv2}') + #for i, data in df_diff_vert.iterrows(): + # if data[0]['self'] != data[0]['other']: + # print(f"{data.name}\t{data[0]['self'] == data[0]['other']}\t{data[0]['self']}\t{data[0]['other']}") + + + count_dict={} + for i in df_comp1.columns: + count_dict[i]=df_comp1[i].value_counts() + counts_df=pd.DataFrame.from_dict(count_dict, orient='columns', dtype=None, columns=None) + print(counts_df) + + + out_xlsx_name=f'{args.outdir}/{args.prefix}.xlsx' + out_html_name=f'{args.outdir}/{args.prefix}.html' + out_pdf_name=f'{args.outdir}/{args.prefix}.pdf' + + pd.set_option('display.max_colwidth', 20) + df_comp1.to_excel(out_xlsx_name) + df_val_cnts.to_html(out_html_name) + + options = { + 'page-width': '10000mm', + 'title': 'Validation Report', + 'margin-top': '0.25in', + 'margin-right': '0.25in', + 'margin-bottom': '0.25in', + 'margin-left': '0.25in'} + out_pdf_var=out_html_name + pdf1 = pdf.from_file(out_html_name, out_pdf_name, options=options) + + + print(df_comp1)