DnaseAlignmentQualityMetric
fourier_transform_eleven
Fourier transform of the insert size at 11 bases
insert_size_histogram
Insert size histogram for all reads
insert_size_metric
Insert size metric file
large_small_ratio
Ratio of long to short reads
nuclear_preseq
Total read metrics file
nuclear_preseq_targets
Sequencing depth file
DnaseFootprintingQualityMetric
footprint_count
Total number of DNaseI footprints
DuplicatesQualityMetric
Reads Examined
Total number of paired and unpaired reads examined
Read Duplicates
Total number of paired and unpaired read duplicates
UMI Read Duplicates
Number of UMI flagged read duplicates
Percent Duplication
Percent of reads that are duplicates
Read Pairs Examined
Number of read pairs examined by picard
Read Pair Duplicates
Number of read pairs detected as duplicates by picard
Read Pair Optical Duplicates
Number of read pairs detected as optical duplicates by picard
Unmapped Reads
Number of unmapped detected by picard
Unpaired Reads Examined
Number of unpaired reads examined by picard
Unpaired Read Duplicates
Number of unpaired reads detected as duplicates by picard
Estimated Library Size
Library size in reads as estimated by picard
HotspotQualityMetric
spot1_score
SPOT score as calculated by Hotspot1
spot2_score
SPOT score as calculated by Hotspot2
hotspot_count
Count of hotspots discovered by Hotspot2
peaks_count
Count of peaks discovered by Hotspot2
total_tags
Count of read tags provided to Hotspot
hotspot_tags
Count of read tags discovered to be in hotspots
five_percent_allcalls_count
Count of five percent calls
five_percent_hotspots_count
Count of five percent hotspots
five_percent_narrowpeaks_count
Count of five percent narrowpeaks
tenth_of_one_percent_narrowpeaks_count
Count of tenth of one percent narrowpeaks
TrimmingQualityMetric
PE read-pairs processed
Total number read-pairs processed
PE read-pairs trimmed
Total number read-pairs trimmed
read_1_with_adapter
Number of read1 with adapter
read_2_with_adapter
Number of read2 with adapter
SE reads processed
Total number (single-end) reads processed
SE reads trimmed
Total number (single-end) reads trimmed
total_read_pairs_processed
Total number read-pairs processed
EdwbamstatsQualityMetric
Deprecated
alignedBy
The aligner used
isPaired
If alignment is from paired-end reads this will be set to 1
isSortedByTarget
If the bam is sorted by target location, this is set to 1; if sorted by name, this is set to 0
mappedCount
Count of mapped reads
readBaseCount
Count of total bases in reads
readCount
Count of all reads
readSizeMax
Longest read
readSizeMean
Mean size of all reads
readSizeMin
Shortest read
readSizeStd
Standard deviation of read size
targetBaseCount
Number of bases covered in target (e.g. on chromosomes)
targetSeqCount
Count of target sequences (e.g. chromosomes)
u4mReadCount
Number of randomly sampled uniquely mapped items used in complexity calculation
u4mUniquePos
Number of unique positions that sampled uniquely mapped reads were mapped to
u4mUniqueRatio
Ratio of unique positions to uniquely mapped reads
uniqueMappedCount
Count of reads uniquely mapped
FilteringQualityMetric
Deprecated
pre-filter all reads
Count of all reads prior to filtering
pre-filter mapped reads
Count of mapped reads prior to filtering
post-filter all reads
Count of all reads after filtering
post-filter mapped reads
Count of mapped reads after filtering