Hs metrics

The HS metrics file consists of one line with lots of metrics, and an histogram

• Basic sequencing metrics that are either generated as a baseline against which to evaluate other metrics or because they are used in the calculation of other metrics. This includes things like the genome size, the number of reads, the number of aligned reads etc.

• Metrics that are intended for evaluating the performance of the wet-lab assay that generated the data. This group includes metrics like the number of bases mapping on/off/near baits, %selected, fold 80 base penalty, hs library size and the hs penalty metrics. These metrics are calculated prior to some of the filters are applied (e.g. low mapping quality reads, low base quality bases and bases overlapping in the middle of paired-end reads are all counted).

• Metrics for assessing target coverage as a proxy for how well the data is likely to perform in downstream applications like variant calling. This group includes metrics like mean target coverage, the percentage of bases reaching various coverage levels, and the percentage of bases excluded by various filters. These metrics are computed using the strictest subset of the data, after all filters have been applied.

	Field	Description
1	BAIT_SET	The name of the bait set used in the hybrid selection.
2	GENOME_SIZE	The number of bases in the reference genome used for alignment.
3	BAIT_TERRITORY	The number of bases which are localized to one or more baits.
4	TARGET_TERRITORY	The unique number of target bases in the experiment, where the target sequence is usually exons etc.
5	BAIT_DESIGN_EFFICIENCY	The ratio of TARGET_TERRITORY/BAIT_TERRITORY. A value of 1 indicates a perfect design efficiency, while a valud of 0.5 indicates that half of bases within the bait region are not within the target region.
6	TOTAL_READS	The total number of reads in the SAM or BAM file examined.
7	PF_READS	The total number of reads that pass the vendor's filter.
8	PF_UNIQUE_READS	The number of PF reads that are not marked as duplicates.
9	PCT_PF_READS	The fraction of reads passing the vendor's filter, PF_READS/TOTAL_READS.
10	PCT_PF_UQ_READS	The fraction of PF_UNIQUE_READS from the TOTAL_READS, PF_UNIQUE_READS/TOTAL_READS.
11	PF_UQ_READS_ALIGNED	The number of PF_UNIQUE_READS that aligned to the reference genome with a mapping score > 0.
12	PCT_PF_UQ_READS_ALIGNED	The fraction of PF_UQ_READS_ALIGNED from the total number of PF reads.
13	PF_BASES_ALIGNED	The number of PF unique bases that are aligned to the reference genome with mapping scores > 0.
14	PF_UQ_BASES_ALIGNED	The number of bases in the PF_UQ_READS_ALIGNED reads. Accounts for clipping and gaps.
15	ON_BAIT_BASES	The number of PF_BASES_ALIGNED that are mapped to the baited regions of the genome.
16	NEAR_BAIT_BASES	The number of PF_BASES_ALIGNED that are mapped to within a fixed interval containing a baited region, but not within the baited section per se.
17	OFF_BAIT_BASES	The number of PF_BASES_ALIGNED that are mapped away from any baited region.
18	ON_TARGET_BASES	The number of PF_BASES_ALIGNED that are mapped to a targeted region of the genome.
19	PCT_SELECTED_BASES	The fraction of PF_BASES_ALIGNED located on or near a baited region (ON_BAIT_BASES + NEAR_BAIT_BASES)/PF_BASES_ALIGNED.
20	PCT_OFF_BAIT	The fraction of PF_BASES_ALIGNED that are mapped away from any baited region, OFF_BAIT_BASES/PF_BASES_ALIGNED.
21	ON_BAIT_VS_SELECTED	The fraction of bases on or near baits that are covered by baits, ON_BAIT_BASES/(ON_BAIT_BASES + NEAR_BAIT_BASES).
22	MEAN_BAIT_COVERAGE	The mean coverage of all baits in the experiment.
23	MEAN_TARGET_COVERAGE	The mean coverage of a target region.
24	MEDIAN_TARGET_COVERAGE	The median coverage of a target region.
25	MAX_TARGET_COVERAGE	The maximum coverage of reads that mapped to target regions of an experiment.
26	PCT_USABLE_BASES_ON_BAIT	The number of aligned, de-duped, on-bait bases out of the PF bases available.
27	PCT_USABLE_BASES_ON_TARGET	The number of aligned, de-duped, on-target bases out of all of the PF bases available.
28	FOLD_ENRICHMENT	The fold by which the baited region has been amplified above genomic background.
29	ZERO_CVG_TARGETS_PCT	The fraction of targets that did not reach coverage=1 over any base.
30	PCT_EXC_DUPE	The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
31	PCT_EXC_MAPQ	The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
32	PCT_EXC_BASEQ	The fraction of aligned bases that were filtered out because they were of low base quality.
33	PCT_EXC_OVERLAP	The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
34	PCT_EXC_OFF_TARGET	The fraction of aligned bases that were filtered out because they did not align over a target base.
35	FOLD_80_BASE_PENALTY	The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.
36	PCT_TARGET_BASES_1X	The fraction of all target bases achieving 1X or greater coverage.
37	PCT_TARGET_BASES_2X	The fraction of all target bases achieving 2X or greater coverage.
38	PCT_TARGET_BASES_10X	The fraction of all target bases achieving 10X or greater coverage.
39	PCT_TARGET_BASES_20X	The fraction of all target bases achieving 20X or greater coverage.
40	PCT_TARGET_BASES_30X	The fraction of all target bases achieving 30X or greater coverage.
41	PCT_TARGET_BASES_40X	The fraction of all target bases achieving 40X or greater coverage.
42	PCT_TARGET_BASES_50X	The fraction of all target bases achieving 50X or greater coverage.
43	PCT_TARGET_BASES_100X	The fraction of all target bases achieving 100X or greater coverage.
44	HS_LIBRARY_SIZE	The estimated number of unique molecules in the selected part of the library.
45	HS_PENALTY_10X	The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric\ should be interpreted as: if I have a design with 10 megabases of target, and want to get\ 10X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 10 * HS_PENALTY_10X.
46	HS_PENALTY_20X	The "hybrid selection penalty" incurred to get 80% of target bases to 20X. This metric\ should be interpreted as: if I have a design with 10 megabases of target, and want to get\ 20X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 20 * HS_PENALTY_20X.
47	HS_PENALTY_30X	The "hybrid selection penalty" incurred to get 80% of target bases to 30X. This metric\ should be interpreted as: if I have a design with 10 megabases of target, and want to get\ 30X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 30 * HS_PENALTY_30X.
48	HS_PENALTY_40X	The "hybrid selection penalty" incurred to get 80% of target bases to 40X. This metric\ should be interpreted as: if I have a design with 10 megabases of target, and want to get\ 40X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 40 * HS_PENALTY_40X.
49	HS_PENALTY_50X	The "hybrid selection penalty" incurred to get 80% of target bases to 50X. This metric\ should be interpreted as: if I have a design with 10 megabases of target, and want to get\ 50X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 50 * HS_PENALTY_50X.
50	HS_PENALTY_100X	The "hybrid selection penalty" incurred to get 80% of target bases to 100X. This metric\ should be interpreted as: if I have a design with 10 megabases of target, and want to get\ 100X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 100 * HS_PENALTY_100X.
51	AT_DROPOUT	A measure of how undercovered <= 50% GC regions are relative to the mean. For each GC bin [0..50]\ we calculate a = % of target territory, and b = % of aligned reads aligned to these targets.\ AT DROPOUT is then abs(sum(a-b when a-b < 0)). E.g. if the value is 5% this implies that 5% of total\ reads that should have mapped to GC<=50% regions mapped elsewhere.
52	GC_DROPOUT	A measure of how undercovered >= 50% GC regions are relative to the mean. For each GC bin [50..100]\ we calculate a = % of target territory, and b = % of aligned reads aligned to these targets.\ GC DROPOUT is then abs(sum(a-b when a-b < 0)). E.g. if the value is 5% this implies that 5% of total\ reads that should have mapped to GC>=50% regions mapped elsewhere.
53	HET_SNP_SENSITIVITY	The theoretical HET SNP sensitivity.
54	HET_SNP_Q	The Phred Scaled Q Score of the theoretical HET SNP sensitivity.