When I piled up an alignment by this command, I received the result in the bottom. What does each column mean? I know "chr_2 5554123" is a SNP.
samtools pileup -c -f ../../ssahaSNP_result/Sorbil.fasta test.bam > test.full.pileup
chr_2 5554119 t T 30 0 60 1 . R
chr_2 5554120 t T 30 0 60 1 . P
chr_2 5554121 t T 30 0 60 1 . A
chr_2 5554122 g G 30 0 60 1 . A
chr_2 5554123 t C 0 2 60 1 C A
chr_2 5554124 a A 30 0 60 1 . X
samtools pileup -c -f ../../ssahaSNP_result/Sorbil.fasta test.bam > test.full.pileup
chr_2 5554119 t T 30 0 60 1 . R
chr_2 5554120 t T 30 0 60 1 . P
chr_2 5554121 t T 30 0 60 1 . A
chr_2 5554122 g G 30 0 60 1 . A
chr_2 5554123 t C 0 2 60 1 C A
chr_2 5554124 a A 30 0 60 1 . X
Comment