Pileup format

samtools

chr1 808922 G A 21 116 53 9 aAaaaaaAA 9=;:@?9:,

chr1 ---> name of this sequence is chr1

808922 ---> coordinate is 808922 (1-based)

G ---> reference base is 'G'

A ---> consensus base is 'A'

21 ---> consensus quality is 21

116 ---> SNP quality is 116

53 ---> maximum mapping quality is 53

9 ---> the number of reads covering the site is 9

aAaaaaaAA ---> read bases are 'aAaaaaaAA'

9=;:@?9:, --->base qualities are '9=;:@?9:,'

consensus quality (21) is the Phred-scaled probability that the consensus is wrong. SNP quality (116) is the Phred-scaled probability that the consensus is identical to the reference.

For SNP calling, SNP quality is of more importance.

For example, to further filter the SNP calls:

samtools.pl varFilter raw.pileup | awk '$6>=20' > final.pileup