public class TargetedPcrMetrics extends MultilevelMetrics
Modifier and Type | Field and Description |
---|---|
long |
AMPLICON_TERRITORY
The number of unique bases covered by the intervals of all amplicons in the amplicon set
|
double |
AT_DROPOUT
A measure of how regions with low GC content (<= 50%), are undercovered relative to mean coverage.
|
java.lang.String |
CUSTOM_AMPLICON_SET
The name of the amplicon set used in this metrics collection run
|
double |
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.
|
double |
FOLD_ENRICHMENT
The fold by which the amplicon region has been amplified above genomic background.
|
double |
GC_DROPOUT
A measure of how regions of high GC content (>= 50% GC) are undercovered relative to the mean coverage
value.
|
long |
GENOME_SIZE
The number of bases in the reference genome used for alignment
|
double |
HET_SNP_Q
The Q Score of the theoretical HET SNP sensitivity.
|
double |
HET_SNP_SENSITIVITY
The theoretical HET SNP sensitivity.
|
double |
MEAN_AMPLICON_COVERAGE
The mean read coverage of all amplicon regions in the experiment.
|
double |
MEAN_TARGET_COVERAGE
The mean read coverage of all target regions in an experiment.
|
double |
MEDIAN_TARGET_COVERAGE
The median coverage of reads that mapped to target regions of an experiment.
|
long |
NEAR_AMPLICON_BASES
The number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a
baited region.
|
long |
OFF_AMPLICON_BASES
The number of PF_BASES_ALIGNED that mapped neither on or near an amplicon.
|
long |
ON_AMPLICON_BASES
The number of PF_BASES_ALIGNED that mapped to an amplified region of the genome.
|
double |
ON_AMPLICON_VS_SELECTED
The fraction of bases mapping to regions on or near amplicons, which mapped directly to but not near
amplicons, ON_AMPLICON_BASES/(NEAR_AMPLICON_BASES + ON_AMPLICON_BASES)
|
long |
ON_TARGET_BASES
The number of PF_BASES_ALIGNED that mapped to a targeted region of the genome.
|
long |
ON_TARGET_FROM_PAIR_BASES
The number of bases from PF_SELECTED_UNIQUE_PAIRS that mapped to a targeted region of the genome.
|
double |
PCT_AMPLIFIED_BASES
The fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES +
NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED.
|
double |
PCT_EXC_BASEQ
The fraction of aligned bases that were filtered out because they were of low base quality.
|
double |
PCT_EXC_DUPE
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
|
double |
PCT_EXC_MAPQ
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
|
double |
PCT_EXC_OFF_TARGET
The fraction of bases that were filtered out because they did not map to a base within a target region.
|
double |
PCT_EXC_OVERLAP
The fraction of aligned bases that were filtered out because they were the second observation from an
insert with overlapping reads.
|
double |
PCT_OFF_AMPLICON
The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon,
OFF_AMPLICON_BASES/PF_BASES_ALIGNED
|
double |
PCT_PF_READS
The fraction of reads passing filter, PF_READS/TOTAL_READS.
|
double |
PCT_PF_UQ_READS
The fraction of TOTAL_READS that are unique, PF, and are not duplicates, PF_UNIQUE_READS/TOTAL_READS
|
double |
PCT_PF_UQ_READS_ALIGNED
Fraction of PF_READS that are unique and align to the reference genome, PF_UQ_READS_ALIGNED/PF_READS
|
double |
PCT_TARGET_BASES_10X
The fraction of all target bases achieving 10X or greater coverage depth.
|
double |
PCT_TARGET_BASES_1X
The fraction of all target bases achieving 1X or greater coverage.
|
double |
PCT_TARGET_BASES_20X
The fraction of all target bases achieving 20X or greater coverage depth.
|
double |
PCT_TARGET_BASES_2X
The fraction of all target bases achieving 2X or greater coverage depth.
|
double |
PCT_TARGET_BASES_30X
The fraction of all target bases achieving 30X or greater coverage depth.
|
long |
PF_BASES
The total number of bases within the PF_READS of the SAM or BAM file to be examined
|
long |
PF_BASES_ALIGNED
The number of bases from PF_READS that align to the reference genome with mapping score > 0
|
long |
PF_READS
The total number of reads passing filter (PF), where the filter(s) can be platform/vendor quality controls
|
long |
PF_SELECTED_PAIRS
Tracks the number of PF read pairs (used to calculate library size)
|
long |
PF_SELECTED_UNIQUE_PAIRS
Tracks the number of unique, PF, read pairs, observed (used to calculate library size)
|
long |
PF_UNIQUE_READS
The number of PF_READS that were not marked as sample or optical duplicates.
|
long |
PF_UQ_BASES_ALIGNED
The number of bases from PF_UNIQUE_READS that align to the reference genome and have a mapping score > 0
|
long |
PF_UQ_READS_ALIGNED
The total number of PF_UNIQUE_READS that align to the reference genome with mapping scores > 0
|
long |
TARGET_TERRITORY
The number of unique bases covered by the intervals of all targets that should be covered
|
long |
TOTAL_READS
The total number of reads in the SAM or BAM file examined
|
double |
ZERO_CVG_TARGETS_PCT
The fraction of targets that did not reach coverage=1 over any base.
|
LIBRARY, READ_GROUP, SAMPLE
Constructor and Description |
---|
TargetedPcrMetrics() |
public java.lang.String CUSTOM_AMPLICON_SET
public long GENOME_SIZE
public long AMPLICON_TERRITORY
public long TARGET_TERRITORY
public long TOTAL_READS
public long PF_READS
public long PF_BASES
public long PF_UNIQUE_READS
public double PCT_PF_READS
public double PCT_PF_UQ_READS
public long PF_UQ_READS_ALIGNED
public long PF_SELECTED_PAIRS
public long PF_SELECTED_UNIQUE_PAIRS
public double PCT_PF_UQ_READS_ALIGNED
public long PF_BASES_ALIGNED
public long PF_UQ_BASES_ALIGNED
public long ON_AMPLICON_BASES
public long NEAR_AMPLICON_BASES
public long OFF_AMPLICON_BASES
public long ON_TARGET_BASES
public long ON_TARGET_FROM_PAIR_BASES
public double PCT_AMPLIFIED_BASES
public double PCT_OFF_AMPLICON
public double ON_AMPLICON_VS_SELECTED
public double MEAN_AMPLICON_COVERAGE
public double MEAN_TARGET_COVERAGE
public double MEDIAN_TARGET_COVERAGE
public double FOLD_ENRICHMENT
public double ZERO_CVG_TARGETS_PCT
public double PCT_EXC_DUPE
public double PCT_EXC_MAPQ
public double PCT_EXC_BASEQ
public double PCT_EXC_OVERLAP
public double PCT_EXC_OFF_TARGET
public double FOLD_80_BASE_PENALTY
public double PCT_TARGET_BASES_1X
public double PCT_TARGET_BASES_2X
public double PCT_TARGET_BASES_10X
public double PCT_TARGET_BASES_20X
public double PCT_TARGET_BASES_30X
public double AT_DROPOUT
public double GC_DROPOUT
public double HET_SNP_SENSITIVITY
public double HET_SNP_Q