Hi, I imported a vcf file containing SNP into IGV v2.12.3, I am using default color setting and color the variant with allele frequency. In the genotype part, which shows cyan (homozygous SNP) or blue (heterozygous SNP) in the variant part, it shows red for alternative allele and blue for reference allele.

But in some case, even the depth bar shows around 50%-50% of alternative and reference allele, but the variant part (circled by red rectangle) is all blue. Is this has something to do with the quality of SNP? since these SNP quality are seems to be low.

In the IGV manual: blue - minor allele frequency/fraction is known from annotation or genotype data grey - minor allele frequency is not known red - height is proportional to minor allele frequency But it is still not clear for me.