AlignmentSummaryMetrics (PICARD JDK API Documentation)

java.lang.Object
- htsjdk.samtools.metrics.MetricBase
- - picard.metrics.MultilevelMetrics
  - - picard.analysis.AlignmentSummaryMetrics

```
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".

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class AlignmentSummaryMetrics.Category

Nested Classes
Modifier and Type	Class and Description
`static class`	`AlignmentSummaryMetrics.Category`

Field Summary

Fields
Modifier and Type	Field and 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 percentage of PF reads that are unaligned and match to a known adapter sequence right from the start of the read.
`double`	`PCT_CHIMERAS` The percentage 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 percentage 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_READS_ALIGNED_IN_PAIRS` The percentage of 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 percentage 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`	`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

Constructor Summary

Constructors
Constructor and Description

AlignmentSummaryMetrics()

Constructors
Constructor and Description
`AlignmentSummaryMetrics()`

Method Summary
- Methods inherited from class htsjdk.samtools.metrics.MetricBase
  equals, hashCode, toString
- Methods inherited from class java.lang.Object
  clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - 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.
  - 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.
  - PF_READS
```
public long PF_READS
```
    The number of PF reads where PF is defined as passing Illumina's filter.
  - PCT_PF_READS
```
public double PCT_PF_READS
```
    The percentage of reads that are PF (PF_READS / TOTAL_READS)
  - 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.
  - 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).
  - 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
  - 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.
  - 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.
  - 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.
  - 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.
  - 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).
  - PF_MISMATCH_RATE
```
public double PF_MISMATCH_RATE
```
    The rate of bases mismatching the reference for all bases aligned to the reference sequence.
  - PF_HQ_ERROR_RATE
```
public double PF_HQ_ERROR_RATE
```
    The percentage of bases that mismatch the reference in PF HQ aligned reads.
  - 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.
  - 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.
  - READS_ALIGNED_IN_PAIRS
```
public long READS_ALIGNED_IN_PAIRS
```
    The number of aligned reads whose mate pair was also aligned to the reference.
  - PCT_READS_ALIGNED_IN_PAIRS
```
public double PCT_READS_ALIGNED_IN_PAIRS
```
    The percentage of reads whose mate pair was also aligned to the reference. READS_ALIGNED_IN_PAIRS / PF_READS_ALIGNED
  - BAD_CYCLES
```
public long BAD_CYCLES
```
    The number of instrument cycles in which 80% or more of base calls were no-calls.
  - 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.
  - PCT_CHIMERAS
```
public double PCT_CHIMERAS
```
    The percentage of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes.
  - PCT_ADAPTER
```
public double PCT_ADAPTER
```
    The percentage of PF reads that are unaligned and match to a known adapter sequence right from the start of the read.
- Constructor Detail
  - AlignmentSummaryMetrics
```
public AlignmentSummaryMetrics()
```

Class AlignmentSummaryMetrics

Nested Class Summary

Field Summary

Fields inherited from class picard.metrics.MultilevelMetrics

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

Methods inherited from class java.lang.Object

Field Detail

CATEGORY

TOTAL_READS

PF_READS

PCT_PF_READS

PF_NOISE_READS

PF_READS_ALIGNED

PCT_PF_READS_ALIGNED

PF_ALIGNED_BASES

PF_HQ_ALIGNED_READS

PF_HQ_ALIGNED_BASES

PF_HQ_ALIGNED_Q20_BASES

PF_HQ_MEDIAN_MISMATCHES

PF_MISMATCH_RATE

PF_HQ_ERROR_RATE

PF_INDEL_RATE

MEAN_READ_LENGTH

READS_ALIGNED_IN_PAIRS

PCT_READS_ALIGNED_IN_PAIRS

BAD_CYCLES

STRAND_BALANCE

PCT_CHIMERAS

PCT_ADAPTER

Constructor Detail

AlignmentSummaryMetrics