Hi, I start working with IGV, but I have some doubts in how to identify a good SPN in this program. First I download the new Soybean Genome on Phytozome (Gmax_275_v2.0.fa and Gmax_275_Wm82.a2.v1.gene.gff3 files), and then I upload my files (sample.vcf, sample.bam and sample.bam.bai) into the program. I indexed which files that program needed, so that's OK! But my doubt is which parameters should I consider for a good SNP? For example, what I need to see on Alleles, Genotypes and Variant Attributes? See the example below.
Chr: Chr06 Position: 35170948 ID: . Reference: C* Alternate: T Qual: 160 Type: SNP Is Filtered Out: No
Alleles: No Call: 0 Allele Num: 2 Allele Count: 4 Allele Frequency: 1
Minor Allele Fraction: 1
Genotypes: Non Variant: 0 - No Call: 0 - Hom Ref: 0 Variant: 1 - Het: 0 - Hom Var: 1
Variant Attributes AF1: 1 RPB: 5.557190e-01 VDB: 1.587578e-01 Depth: 18 FQ: -54 DP4: [1, 1, 6, 8] AC1: 2 Mapping Quality: 25 PV4: [1, 0.22, 1, 0.24]