Map / Align Metrics
Mapping and aligning metrics, unless explicitly stated, are in reads (not in terms of pairs or alignments).
The following metrics are reported:
|
Statistic |
Description |
|---|---|
|
Total input reads |
Total number of reads in the input FASTQs. |
|
Number of duplicate marked reads |
Number of reads marked as duplicate. |
|
Number of duplicate marked and mate reads removed |
Number of duplicate reads discarded. |
|
Number of unique reads (excl. duplicate marked reads) |
Total number of reads minus the duplicate marked reads. |
|
Reads with mate sequenced |
The number of reads with a mate. |
|
Reads without mate sequenced |
The total number of reads minus the reads with mate sequenced. |
|
QC-failed reads |
Reads not passing platform/ vendor quality checks (SAM flag 0x200). |
|
Mapped reads |
The total number of mapped reads minus the number of unmapped reads. |
|
Unmapped reads |
The total number of reads that could not be mapped. |
|
Singleton reads (itself mapped; mate unmapped) |
The number of reads, where the read could be mapped, but the paired mate could not. |
|
Paired reads (itself & mate mapped) |
Both reads in the pair are mapped. |
|
Properly paired reads |
Both reads in the pair are mapped and fall within an acceptable range from each other based on the estimated insert length distribution. |
|
Not properly paired reads (discordant) |
The number of paired reads minus the number of properly paired reads. |
|
Reads with MAPQ [40:inf) |
The number of reads with a MAPQ value greater than or equal to 40. |
|
Reads with MAPQ [30:40) |
The number of reads with a MAPQ value greater than or equal to 30 and less than 40. |
|
Reads with MAPQ [20:30) |
The number of reads with a MAPQ value greater than or equal to 20 and less than 30. |
|
Reads with MAPQ [10:20) |
The number of reads with a MAPQ value greater than or equal to 10 and less than 20. |
|
Reads with MAPQ [0:10) |
The number of reads with a MAPQ value greater than or equal to 0 and less than 10. |
|
Reads with MAPQ NA (Unmapped reads) |
Total number of reads without a MAPQ value. |
|
Reads with indel R1 |
The percentage of R1 reads containing at least 1 indel. |
|
Reads with indel R2 |
The percentage of R2 reads containing at least 1 indel. |
|
Soft-clipped bases R1 |
The percentage of bases in R1 reads that are soft clipped. |
|
Soft-clipped bases R2 |
The percentage of bases in R2 reads that are soft clipped. |
|
Total alignments |
Total number of loci reads aligned to with > 0 quality. |
|
Secondary alignments |
Number of secondary alignment loci. |
|
Supplementary (chimeric) alignments |
A chimeric read is split over multiple loci (possibly due to structural variants). One alignment is referred to as the representative alignment, the other are supplementary. |
|
Estimated read length |
Total number of input bases divided by the number of reads. |
|
Bases in reference genome |
Total number of bases in the reference genome. |
|
Bases in target bed [% of genome] |
Total number of bases in the target region |
|
Average sequenced coverage over genome |
Total number of reads times the average read length divided by the total number of loci in the genome. |
|
Average alignment coverage over genome |
Total number of aligned bases divided by the total number of loci in the genome. |
|
PCT of genome with coverage [100x:inf) |
Percentage of bases in the genome with a range of coverage greater than or equal to 100x. |
|
PCT of genome with coverage [50x:100x) |
Percentage of bases in the genome with a range of coverage greater than or equal to 50x and less than 100x. |
|
PCT of genome with coverage [20x:50x) |
Percentage of bases in the genome with a range of coverage greater than or equal to 20x and less than 50x. |
|
PCT of genome with coverage [10x:20x) |
Percentage of bases in the genome with a range of coverage greater than or equal to 10x and less than 20x. |
|
PCT of genome with coverage [3x:10x) |
Percentage of bases in the genome with a range of coverage greater than or equal to 3x and less than 10x. |
|
PCT of genome with coverage [0x:3x) |
Percentage of bases in the genome with a range of coverage greater than or equal to 0x and less than 3x. |
|
Average chr X coverage |
Total number of bases that aligned to chromosome X (or to the intersection of chromosome X with the target region) divided by the total number of loci in chromosome X (or to the intersection of chromosome X with the target region). If there is no chromosome X in the reference genome, this metric shows as NA. |
|
Average chr Y coverage |
Total number of bases that aligned to chromosome Y (or to the intersection of chromosome Y with the target region) divided by the total number of loci in chromosome Y (or in the intersection of chromosome Y with the target region). If there is no chromosome Y in the reference genome, this metric shows as NA. |
|
Average mitochondrial coverage |
Total number of bases that aligned to the mitochondrial chromosome (or to the intersection of the mitochondrial chromosome with the target region) divided by the total number of loci in the mitochondrial chromosome (or in the intersection of the mitochondrial chromosome with the target region). If there was no mitochondrial chromosome in the reference genome, this metric shows as NA. |
|
Average autosomal coverage |
Total number of bases that aligned to autosomes (or to the autosomal loci in the target region) divided by the total number of loci in the autosomes (or to the autosomal loci in the target region). If there was no autosome in the reference genome, this metric shows as NA. |
|
Median autosomal coverage |
Median alignment coverage over the autosomes (or over the autosomal loci in the target region). If there was no autosome in the reference genome, this metric shows as NA. |
|
Mean/Median autosomal coverage ratio |
Mean autosomal coverage in the genome (or in the target region) divided by the median autosomal coverage in the genome (or in the target region). If there was no autosome in the reference genome, this metric shows as NA. |
|
XAvgCov/YAvgCov ratio |
Average chromosome X alignment coverage in the genome (or in the target region) divided by the average chromosome Y alignment coverage in the genome (or in the target region). If there was chromosome X or chromosome Y in the reference genome, this metric shows as NA. |
|
XAvgCov/AutosomalAvgCov ratio |
Average chromosome X alignment coverage in the genome (or in the target region) divided by the average autosomal coverage in the genome (or in the target region). |
|
Provided sex chromosome ploidy |
The specified sex chromosome of the sample (if entered). |
|
Predicted sex chromosome ploidy |
The sex chromosome of the sample as determined through the analysis. |
|
Capture Specificity based on target region |
Number of unique (nonduplicate) reads that mapped inside the target region with a MAP quality greater than 0, divided by the number of unique (nonduplicate) reads that mapped anywhere in the reference with a MAP quality greater than 0. |
|
DRAGEN mapping rate [mil. reads/second] |
The rate at which the pipeline generates seeds from the read and looks for exact matches in the reference genome. |
|
Total reads in RG |
Total number of reads in the read group. |
|
Insert length: mean |
The average length of the sequence in between a pair of reads. |
|
Insert length: standard deviation |
The standard deviation of the length of the sequence in between a pair of reads. |