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Identifying good SNPs

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

No Call: 0
Allele Num: 2
Allele Count: 4
Allele Frequency: 1

Minor Allele Fraction: 1

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]



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