Why 0/0 genotype refers to SNP and ALT != REF (in vcf file after freebayes)

Question

[poecile.pal]

Good morning,

Could you please explain me, why 0/0 genotypes in vcf are SNPs? According to this description of GT:

0/0 the sample is a homozygous reference
0/1 the sample is heterozygous (carries both reference and alternate alleles)
1/1 the sample is a homozygous alternate
./. No genotype called or missing genotype

Based on this, I should not expect differences from the reference in both alleles. So why ALT nucleotide is not similar to REF nucleotide? And why 0/0 genotype is SNP in general?

Chr1    1677    .   A   C   0   .   AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=3.0103;EPPR=5.06748;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=50.4829;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=26;QR=1406;RO=38;RPL=1;RPP=3.0103;RPPR=14.2105;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=8;SRP=30.668;SRR=30;TYPE=snp   GT:GQ:DP:AD:RO:QR:AO:QA:GL  0/0:160.002:40:38,2:38:1406:2:26:0,-9.57122,-124.366

(example from .vcf file generated by freebayes)

Thank you in advance!

Best regards, Poecile

Answer 1

[poecile.pal]

Maybe I guessed it.

Looking through the mapping in IGV, I see that in this position 1677 most of the reads do not differ from the reference, that is, they have REF nucleotide A. But 2 reads have ALT nucleotide C. This is not enough to name it SNP, since they do not have sufficient statistical support (perhaps this is a sequencing error of these 2 reads). But freebayes is obliged to specify C in the ALT position.