Hi,
I am using SNPs and INDELs data from the mouse genomes project and the data seem to have conflicting information. I mean, seems they report a SNP in a deleted position.
Thus my question,
Is it possible that there are SNPs at positions that are marked as deletions?
As an example, according to mgp.v3.indels.rsIDdbSNPv137.vcf CASTEiJ is homozygous for the deletion starting at position chr19:3372820, listed below (between **):
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASTEiJ
19 3372820 . TCATATGCACCCTCACCTCACACACCC T 191.83 PASS AC1=1;AC=12;AF1=1;AN=12;DP4=1,0,46,40;DP=204;INDEL;MDV=99;MQ=27;MSD=20;PV0=1;PV1=1;PV2=0.0096;PV3=1;PV4=1,1,0.0096,1;QD=0.0088;SB=0.5625;VDB=0.0404;CSQ=ENSMUST00000025835:ENSMUSG00000024900:intron_variant,feature_truncation:Allele,T:Gene,Cpt1a GT:GQ:DP:SP:PL:FI **1/1:99:10:0:183,30,0:1**
At the same time, according to mgp.v3.snps.rsIDdbSNPv137.vcf CASTEiJ is homozygous for a SNP at position chr19:3372824 (between **)
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASTEiJ
19 3372824 rs264849569 A G 199.78 PASS AC1=0;AC=12;AF1=0;AN=36;DP4=299,271,52,63;DP=782;MDV=99;MQ=54;MSD=21;PV0=1;PV1=0.38;PV2=1;PV3=0.12;PV4=1,0.38,1,0.12;QD=0.1029;SB=0.4375;VDB=0.0144;CSQ=ENSMUST00000025835:ENSMUSG00000024900:intron_variant:Allele,G:Gene,Cpt1a GT:GQ:DP:SP:PL:FI **1/1:99:21:0:2 ...