why snp-sites generated variations numbers different snippy mapping results

[Zjianglin]

Hi,

I have some bacterial NGS reads as well as assemblies. I used two methods to call variations:

1. mapping-based: I use clean reads with snippy and reference genome to call variation, and bcftools merge to combined the variations from multiple samples.
2. assembly-based: I assemblied the sample using shovill, annotated them using prokka, got pan-genome results using Panaroo, generated a recombination-free core-genes alignment using ClonalFrameML. Then I get the core genome variations using snp-sites by snp-sites -v -o ours_core_variations.vcf ../PGout_panaroo/core_gene_alignment_filtered.aln

Here is the statistics for two vcfs:

# for merged VCF from individually calling by snippy
1. $ bcftools stats ../Ours_vcf_merged.vcf.gz | grep SN
# SN, Summary numbers:
#   number of SNPs      .. number of rows with a SNP
#   number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#   counter. For example, a row with a SNP and an indel increments both the SNP and
# SN	[2]id	[3]key	[4]value
SN	0	number of samples:	196
SN	0	number of records:	2292
SN	0	number of no-ALTs:	0
SN	0	number of SNPs:	2053
SN	0	number of MNPs:	47
SN	0	number of indels:	180
SN	0	number of others:	13
SN	0	number of multiallelic sites:	13
SN	0	number of multiallelic SNP sites:	1

#for snp-sites results
2. $ bcftools stats ours_core_variations.vcf | grep SN
# SN, Summary numbers:
#   number of SNPs      .. number of rows with a SNP
#   number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
#   counter. For example, a row with a SNP and an indel increments both the SNP and
# SN	[2]id	[3]key	[4]value
SN	0	number of samples:	196
SN	0	number of records:	5907
SN	0	number of no-ALTs:	0
SN	0	number of SNPs:	5907
SN	0	number of MNPs:	0
SN	0	number of indels:	0
SN	0	number of others:	0
SN	0	number of multiallelic sites:	3408
SN	0	number of multiallelic SNP sites:	34

There is a huge difference between the total variations (2292 vs. 5907) as well as SNP(2053 vs. 5907). Is there anything I did wrong? Could you please help me figure it out?