Package picard.analysis
Class AlignmentSummaryMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.metrics.MultilevelMetrics
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- picard.analysis.AlignmentSummaryMetrics
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public class AlignmentSummaryMetrics extends MultilevelMetrics
High level metrics about the alignment of reads within a SAM file, produced by the CollectAlignmentSummaryMetrics program and usually stored in a file with the extension ".alignment_summary_metrics".
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
AlignmentSummaryMetrics.Category
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Field Summary
Fields Modifier and Type Field Description long
BAD_CYCLES
The number of instrument cycles in which 80% or more of base calls were no-calls.AlignmentSummaryMetrics.Category
CATEGORY
One of either UNPAIRED (for a fragment run), FIRST_OF_PAIR when metrics are for only the first read in a paired run, SECOND_OF_PAIR when the metrics are for only the second read in a paired run or PAIR when the metrics are aggregated for both first and second reads in a pair.double
MEAN_READ_LENGTH
The mean read length of the set of reads examined.double
PCT_ADAPTER
The fraction of PF reads that are unaligned and match to a known adapter sequence right from the start of the read.double
PCT_CHIMERAS
The fraction of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes.double
PCT_PF_READS
The fraction of reads that are PF (PF_READS / TOTAL_READS)double
PCT_PF_READS_ALIGNED
The percentage of PF reads that aligned to the reference sequence.double
PCT_PF_READS_IMPROPER_PAIRS
The fraction of (primary) reads that are *not* "properly" aligned in pairs (as per SAM flag 0x2).double
PCT_READS_ALIGNED_IN_PAIRS
The fraction of aligned reads whose mate pair was also aligned to the reference.long
PF_ALIGNED_BASES
The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence.long
PF_HQ_ALIGNED_BASES
The number of bases aligned to the reference sequence in reads that were mapped at high quality.long
PF_HQ_ALIGNED_Q20_BASES
The subset of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher.long
PF_HQ_ALIGNED_READS
The number of PF reads that were aligned to the reference sequence with a mapping quality of Q20 or higher signifying that the aligner estimates a 1/100 (or smaller) chance that the alignment is wrong.double
PF_HQ_ERROR_RATE
The fraction of bases that mismatch the reference in PF HQ aligned reads.double
PF_HQ_MEDIAN_MISMATCHES
The median number of mismatches versus the reference sequence in reads that were aligned to the reference at high quality (i.e.double
PF_INDEL_RATE
The number of insertion and deletion events per 100 aligned bases.double
PF_MISMATCH_RATE
The rate of bases mismatching the reference for all bases aligned to the reference sequence.long
PF_NOISE_READS
The number of PF reads that are marked as noise reads.long
PF_READS
The number of PF reads where PF is defined as passing Illumina's filter.long
PF_READS_ALIGNED
The number of PF reads that were aligned to the reference sequence.long
PF_READS_IMPROPER_PAIRS
The number of (primary) aligned reads that are **not** "properly" aligned in pairs (as per SAM flag 0x2).long
READS_ALIGNED_IN_PAIRS
The number of aligned reads whose mate pair was also aligned to the reference.double
STRAND_BALANCE
The number of PF reads aligned to the positive strand of the genome divided by the number of PF reads aligned to the genome.long
TOTAL_READS
The total number of reads including all PF and non-PF reads.-
Fields inherited from class picard.metrics.MultilevelMetrics
LIBRARY, READ_GROUP, SAMPLE
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Constructor Summary
Constructors Constructor Description AlignmentSummaryMetrics()
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Field Detail
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CATEGORY
public AlignmentSummaryMetrics.Category CATEGORY
One of either UNPAIRED (for a fragment run), FIRST_OF_PAIR when metrics are for only the first read in a paired run, SECOND_OF_PAIR when the metrics are for only the second read in a paired run or PAIR when the metrics are aggregated for both first and second reads in a pair.
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TOTAL_READS
public long TOTAL_READS
The total number of reads including all PF and non-PF reads. When CATEGORY equals PAIR this value will be 2x the number of clusters.
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PF_READS
public long PF_READS
The number of PF reads where PF is defined as passing Illumina's filter.
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PCT_PF_READS
public double PCT_PF_READS
The fraction of reads that are PF (PF_READS / TOTAL_READS)
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PF_NOISE_READS
public long PF_NOISE_READS
The number of PF reads that are marked as noise reads. A noise read is one which is composed entirely of A bases and/or N bases. These reads are marked as they are usually artifactual and are of no use in downstream analysis.
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PF_READS_ALIGNED
public long PF_READS_ALIGNED
The number of PF reads that were aligned to the reference sequence. This includes reads that aligned with low quality (i.e. their alignments are ambiguous).
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PCT_PF_READS_ALIGNED
public double PCT_PF_READS_ALIGNED
The percentage of PF reads that aligned to the reference sequence. PF_READS_ALIGNED / PF_READS
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PF_ALIGNED_BASES
public long PF_ALIGNED_BASES
The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence.
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PF_HQ_ALIGNED_READS
public long PF_HQ_ALIGNED_READS
The number of PF reads that were aligned to the reference sequence with a mapping quality of Q20 or higher signifying that the aligner estimates a 1/100 (or smaller) chance that the alignment is wrong.
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PF_HQ_ALIGNED_BASES
public long PF_HQ_ALIGNED_BASES
The number of bases aligned to the reference sequence in reads that were mapped at high quality. Will usually approximate PF_HQ_ALIGNED_READS * READ_LENGTH but may differ when either mixed read lengths are present or many reads are aligned with gaps.
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PF_HQ_ALIGNED_Q20_BASES
public long PF_HQ_ALIGNED_Q20_BASES
The subset of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher.
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PF_HQ_MEDIAN_MISMATCHES
public double PF_HQ_MEDIAN_MISMATCHES
The median number of mismatches versus the reference sequence in reads that were aligned to the reference at high quality (i.e. PF_HQ_ALIGNED READS).
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PF_MISMATCH_RATE
public double PF_MISMATCH_RATE
The rate of bases mismatching the reference for all bases aligned to the reference sequence.
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PF_HQ_ERROR_RATE
public double PF_HQ_ERROR_RATE
The fraction of bases that mismatch the reference in PF HQ aligned reads.
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PF_INDEL_RATE
public double PF_INDEL_RATE
The number of insertion and deletion events per 100 aligned bases. Uses the number of events as the numerator, not the number of inserted or deleted bases.
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MEAN_READ_LENGTH
public double MEAN_READ_LENGTH
The mean read length of the set of reads examined. When looking at the data for a single lane with equal length reads this number is just the read length. When looking at data for merged lanes with differing read lengths this is the mean read length of all reads.
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READS_ALIGNED_IN_PAIRS
public long READS_ALIGNED_IN_PAIRS
The number of aligned reads whose mate pair was also aligned to the reference.
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PCT_READS_ALIGNED_IN_PAIRS
public double PCT_READS_ALIGNED_IN_PAIRS
The fraction of aligned reads whose mate pair was also aligned to the reference. READS_ALIGNED_IN_PAIRS / PF_READS_ALIGNED
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PF_READS_IMPROPER_PAIRS
public long PF_READS_IMPROPER_PAIRS
The number of (primary) aligned reads that are **not** "properly" aligned in pairs (as per SAM flag 0x2).
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PCT_PF_READS_IMPROPER_PAIRS
public double PCT_PF_READS_IMPROPER_PAIRS
The fraction of (primary) reads that are *not* "properly" aligned in pairs (as per SAM flag 0x2). PF_READS_IMPROPER_PAIRS / PF_READS_ALIGNED
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BAD_CYCLES
public long BAD_CYCLES
The number of instrument cycles in which 80% or more of base calls were no-calls.
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STRAND_BALANCE
public double STRAND_BALANCE
The number of PF reads aligned to the positive strand of the genome divided by the number of PF reads aligned to the genome.
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PCT_CHIMERAS
public double PCT_CHIMERAS
The fraction of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes.
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PCT_ADAPTER
public double PCT_ADAPTER
The fraction of PF reads that are unaligned and match to a known adapter sequence right from the start of the read.
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