Changes

Qplot process each aligned bam files.

Qplot process each aligned bam files.

(1) Empirical vs reported Phred score:

(1) Empirical vs reported Phred score:

Conditioning on the reported base quality, we count the total time of bases that matches or not matches the reference genome, and thus calculate the empirical quality by : -10 * log10 ( 1 - total # of mismatched / total bases) . In following cases, we will not use that bases for calculating empirical qualities:

Conditioning on the reported base quality, we count the total time of bases that matches or not matches the reference genome, and thus calculate the empirical quality by : -10 * log10 ( 1 - total # of mismatched / total bases) . In following cases, we will not use that bases for calculating empirical qualities:

(a) 'N' for either sequence read or reference genome,

(a) 'N' for either sequence read or reference genome,

(b) sequence reads that have sam flags including duplicated, unmapped

(b) sequence reads that have sam flags including duplicated, unmapped

(c) overlapping dbSNP sites (if dbSNP position file provided)

(c) overlapping dbSNP sites (if dbSNP position file provided)

If specifying --regions, only bases in the target regions will be calculated.

If specifying --regions, only bases in the target regions will be calculated.