3,045
edits
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*TotalBases - # of bases in all reads
*TotalBases - # of bases in all reads
*BasesInMappedReads - # of bases in reads marked mapped in the flag
*BasesInMappedReads - # of bases in reads marked mapped in the flag
== Qual/Phred ==
== Qual/Phred ==
*AverageMapQualCount - # of mapping qualities used to calculate AverageMapQuality.
*AverageMapQualCount - # of mapping qualities used to calculate AverageMapQuality.
Currently there is no special logic to exclude positions where the refernce is 'N'.
Currently there is no special logic to exclude reads from the counts when the base is 'N'.
=== Output Format ====
Order:
*chrom - Chromosome/reference name string from the SAM/BAM
*chromStart - 0-based start position
*chromEnd - 0-based end position (always 1 greater than start and not included in this region)
*Depth - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ below the min
*Q20Bases - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ below the min
*Q20BasesPct(%) - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ below the min
*TotalReads - only excludes clips
*MappedBases - only excludes clips
*MappingRate(%) - only excludes clips
*MapRate_MQPass(%) - only excludes clips
*ZeroMapQual(%) - only excludes clips
*MapQual<10(%) - only excludes clips
*PairedReads(%) - only excludes clips
*ProperPaired(%) - only excludes clips
*DupRate(%) - only excludes clips
*QCFailRate(%) - only excludes clips
*AverageMapQuality - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ 255
*AverageMapQualCount - excludes unmapped reads, duplicates, failed QC, deletions/skips (only CIGAR M/X/= are included), MapQ 255
=== Sample Output ===
=== Sample Output ===
