Short read aligner comparison
From CSBLwiki
http://iga-rna.sourceforge.net/
http://samtools.sourceforge.net/swlist.shtml
http://bamview.sourceforge.net/
This is explained in the manual page. Or briefly (when you invoke pileup with the -c option):
- reference sequence name
- reference coordinate
- reference base, or `*' for an indel line
- genotype where heterozygotes are encoded in the IUB code: M=A/C, R=A/G, W=A/T, S=C/G, Y=C/T and K=G/T; indels are indicated by, for example, */+A, -A/* or +CC/-C. There is no difference between */+A or +A/*.
- Phred-scaled likelihood that the genotype is wrong, which is also called `consensus quality'.
- Phred-scaled likelihood that the genotype is identical to the reference, which is also called `SNP quality'. Suppose the reference base is A and in alignment we see 17 G and 3 A. We will get a low consensus quality because it is difficult to distinguish an A/G heterozygote from a G/G homozygote. We will get a high SNP quality, though, because the evidence of a SNP is very strong.
- root mean square (RMS) mapping quality
- # reads covering the position
- read bases at a SNP line (check the manual page for more information); the 1st indel allele otherwise
- base quality at a SNP line; the 2nd indel allele otherwise
- indel line only: # reads directly supporting the 1st indel allele
- indel line only: # reads directly supporting the 2nd indel allele
- indel line only: # reads supporting a third indel allele
If pileup is invoked without `-c', indel lines and columns between 3 and 7 inclusive will not be outputted.