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Table 2 The first five rows of the GATK4 output file

From: PyBSASeq: a simple and effective algorithm for bulked segregant analysis with whole-genome sequencing data

CHROMaPOSbREFcALTd834927.ADe834927.GQf834931.ADe834931.GQf
129,759CG0,260,26
131,071AG25,399933,2999
131,478CT27,389948,3299
133,667AG21,469939,3299
134,057CT29,379932,3199
  1. aThe chromosome on which the SNP is located
  2. bThe position of the SNP on the chromosome
  3. cThe base sequence of the SNP that is the same as the one from the reference genome
  4. dThe base sequence that is different from REF
  5. eThe allele depths (AD) of the SNP in the first bulk (ID: 834927) or the second bulk (ID: 834931). This column contains two numbers, the first one is the REF read (ADREF) and the second is the ALT read (ADALT)
  6. fThe genotype quality of the SNP in the first bulk (ID: 834927) or the second bulk (ID: 834931)