[Total] Raw Reads (All reads) // All reads in the bam file(s). [Total] QC Fail reads // Reads number failed QC, this flag is marked by other software,like bwa. See flag in the bam structure. [Total] Raw Data(Mb) // Total reads data in the bam file(s). [Total] Paired Reads // Paired reads numbers. [Total] Mapped Reads // Mapped reads numbers. [Total] Fraction of Mapped Reads // Ratio of mapped reads against raw reads. [Total] Mapped Data(Mb) // Mapped data in the bam file(s). [Total] Fraction of Mapped Data(Mb) // Ratio of mapped data against raw data. [Total] Properly paired // Paired reads with properly insert size. See bam format protocol for details. [Total] Fraction of Properly paired // Ratio of properly paired reads against mapped reads [Total] Read and mate paired // Read (read1) and mate read (read2) paired. [Total] Fraction of Read and mate paired // Ratio of read and mate paired against mapped reads [Total] Singletons // Read mapped but mate read unmapped, and vice versa. [Total] Read and mate map to diff chr // Read and mate read mapped to different chromosome, usually because mapping error and structure variants. [Total] Read1 // First reads in mate paired sequencing [Total] Read2 // Mate reads [Total] Read1(rmdup) // First reads after remove duplications. [Total] Read2(rmdup) // Mate reads after remove duplications. [Total] forward strand reads // Number of forward strand reads. [Total] backward strand reads // Number of backward strand reads. [Total] PCR duplicate reads // PCR duplications. [Total] Fraction of PCR duplicate reads // Ratio of PCR duplications. [Total] Map quality cutoff value // Cutoff map quality score, this value can be set by -q. default is 20, because some variants caller like GATK only consider high quality reads. [Total] MapQuality above cutoff reads // Number of reads with higher or equal quality score than cutoff value. [Total] Fraction of MapQ reads in all reads // Ratio of reads with higher or equal Q score against raw reads. [Total] Fraction of MapQ reads in mapped reads // Ratio of reads with higher or equal Q score against mapped reads. [Target] Target Reads // Number of reads covered target region (specified by bed file). [Target] Fraction of Target Reads in all reads // Ratio of target reads against raw reads. [Target] Fraction of Target Reads in mapped reads // Ratio of target reads against mapped reads. [Target] Target Data(Mb) // Total bases covered target region. If a read covered target region partly, only the covered bases will be counted. [Target] Target Data Rmdup(Mb) // Total bases covered target region after remove PCR duplications. [Target] Fraction of Target Data in all data // Ratio of target bases against raw bases. [Target] Fraction of Target Data in mapped data // Ratio of target bases against mapped bases. [Target] Len of region // The length of target regions. [Target] Average depth // Average depth of target regions. Calculated by "target bases / length of regions". [Target] Average depth(rmdup) // Average depth of target regions after remove PCR duplications. [Target] Coverage (>0x) // Ratio of bases with depth greater than 0x in target regions, which also means the ratio of covered regions in target regions. [Target] Coverage (>=4x) // Ratio of bases with depth greater than or equal to 4x in target regions. [Target] Coverage (>=10x) // Ratio of bases with depth greater than or equal to 10x in target regions. [Target] Coverage (>=30x) // Ratio of bases with depth greater than or equal to 30x in target regions. [Target] Coverage (>=100x) // Ratio of bases with depth greater than or equal to 100x in target regions. [Target] Coverage (>=Nx) // This is addtional line for user self-defined cutoff value, see --cutoffdepth [Target] Target Region Count // Number of target regions. In normal practise,it is the total number of exomes. [Target] Region covered > 0x // The number of these regions with average depth greater than 0x. [Target] Fraction Region covered > 0x // Ratio of these regions with average depth greater than 0x. [Target] Fraction Region covered >= 4x // Ratio of these regions with average depth greater than or equal to 4x. [Target] Fraction Region covered >= 10x // Ratio of these regions with average depth greater than or equal to 10x. [Target] Fraction Region covered >= 30x // Ratio of these regions with average depth greater than or equal to 30x. [Target] Fraction Region covered >= 100x // Ratio of these regions with average depth greater than or equal to 100x. [flank] flank size // The flank size will be count. 200 bp in default. Oligos could also capture the nearby regions of target regions. [flank] Len of region (not include target region) // The length of flank regions (target regions will not be count). [flank] Average depth // Average depth of flank regions. [flank] flank Reads // The total number of reads covered the flank regions. Note: some reads covered the edge of target regions, will be count in flank regions also. [flank] Fraction of flank Reads in all reads // Ratio of reads covered in flank regions against raw reads. [flank] Fraction of flank Reads in mapped reads // Ration of reads covered in flank regions against mapped reads. [flank] flank Data(Mb) // Total bases in the flank regions. [flank] Fraction of flank Data in all data // Ratio of total bases in the flank regions against raw data. [flank] Fraction of flank Data in mapped data // Ratio of total bases in the flank regions against mapped data. [flank] Coverage (>0x) // Ratio of flank bases with depth greater than 0x. [flank] Coverage (>=4x) // Ratio of flank bases with depth greater than or equal to 4x. [flank] Coverage (>=10x) // Ratio of flank bases with depth greater than or equal to 10x. [flank] Coverage (>=30x) // Ratio of flank bases with depth greater than or equal to 30x.
