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id

String

The read alignment ID. This ID is unique within the read group this alignment belongs to. For performance reasons, this field may be omitted by a backend. If provided, its intended use is to make caching and UI display easier for genome browsers and other lightweight clients.

read_group_id

String

The ID of the read group this read belongs to. Every read must belong to exactly one read group.

fragment_name

String

The fragment name. Equivalent to QNAME (query template name) in SAM.

improper_placement

boolean

The orientation and the distance between reads from the fragment are inconsistent with the sequencing protocol (inverse of SAM flag 0x2).

duplicate_fragment

boolean

The fragment is a PCR or optical duplicate (SAM flag 0x400).

number_reads

int

The number of reads in the fragment (extension to SAM flag 0x1).

fragment_length

int

The observed length of the fragment, equivalent to TLEN in SAM.

read_number

int

he read ordinal in the fragment, 0-based and less than numberReads. This field replaces SAM flag 0x40 and 0x80 and is intended to more cleanly represent multiple reads per fragment.

failed_vendor_quality_checks

boolean

The read fails platform or vendor quality checks (SAM flag 0x200).

alignment

LinearAlignment

A linear alignment describes the alignment of a read to a Reference, using a position and CIGAR array.

position

Position

The position of this alignment: an unoriented base in some Reference. A Position is represented by a reference name and a base number on that reference (0-based).",

referenceName

String

The name of the Reference on which the Position is located.

position

long

The 0-based offset from the start of the forward strand for that Reference. Genomic positions are non-negative integers less than Reference length.

strand

Strand

Indicates the DNA strand associate for some data item.

NEG_STRAND	The negative (-) strand.
POS_STRAND	The postive (+) strand.

mappingQuality

int

The mapping quality of this alignment, meaning the likelihood that the read maps to this position. Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to the nearest integer.

cigar

List<CigarUnit>

A list of structures for an instance of a CIGAR operation.

operation

CigarOperation

An enum for the different types of CIGAR alignment operations that exist.\\nUsed wherever CIGAR alignments are used. The different enumerated values\\nhave the following usage:

ALIGNMENT_MATCH
INSERT
DELETE
SKIP
CLIP_SOFT
CLIP_HARD
PAD
SEQUENCE_MATCH
SEQUENCE_MISMATCH

* `ALIGNMENT_MATCH`: An alignment match indicates that a sequence can be\\n aligned to the reference without evidence of an INDEL. Unlike the\\n `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators, the `ALIGNMENT_MATCH`\\n operator does not indicate whether the reference and read sequences are an\\n exact match. This operator is equivalent to SAM's `M`.\\n* `INSERT`: The insert operator indicates that the read contains evidence of\\n bases being inserted into the reference. This operator is equivalent to\\n SAM's `I`.\\n* `DELETE`: The delete operator indicates that the read contains evidence of\\n bases being deleted from the reference. This operator is equivalent to\\n SAM's `D`.\\n* `SKIP`: The skip operator indicates that this read skips a long segment of\\n the reference, but the bases have not been deleted. This operator is\\n commonly used when working with RNA-seq data, where reads may skip long\\n segments of the reference between exons. This operator is equivalent to\\n SAM's 'N'.\\n* `CLIP_SOFT`: The soft clip operator indicates that bases at the start/end\\n of a read have not been considered during alignment. This may occur if the\\n majority of a read maps, except for low quality bases at the start/end of\\n a read. This operator is equivalent to SAM's 'S'. Bases that are soft clipped\\n will still be stored in the read.\\n* `CLIP_HARD`: The hard clip operator indicates that bases at the start/end of\\n a read have been omitted from this alignment. This may occur if this linear\\n alignment is part of a chimeric alignment, or if the read has been trimmed\\n (e.g., during error correction, or to trim poly-A tails for RNA-seq). This\\n operator is equivalent to SAM's 'H'.\\n* `PAD`: The pad operator indicates that there is padding in an alignment.\\n This operator is equivalent to SAM's 'P'.\\n* `SEQUENCE_MATCH`: This operator indicates that this portion of the aligned\\n sequence exactly matches the reference (e.g., all bases are equal to the\\n reference bases). This operator is equivalent to SAM's '='.\\n* `SEQUENCE_MISMATCH`: This operator indicates that this portion of the\\n aligned sequence is an alignment match to the reference, but a sequence\\n mismatch (e.g., the bases are not equal to the reference). This can\\n indicate a SNP or a read error. This operator is equivalent to SAM's 'X'.\",\"symbols\":[\"ALIGNMENT_MATCH\",\"INSERT\",\"DELETE\",\"SKIP\",\"CLIP_SOFT\",\"CLIP_HARD\",\"PAD\",\"SEQUENCE_MATCH\",\"SEQUENCE_MISMATCH\"]},\"doc\":\"The operation type.\"},

operationLength

long

referenceSequence

String

f

boolean

f

boolean

f

boolean

f

boolean

type

VariantType

Type of variant, the accepted types and Sequence Ontology (SO) terms are:

SNV	SO:0001483
SNP	SO:0000694
MNV	SO:0002007
MNP	SO:0001013
INDEL	SO:1000032
INSERTION	SO:0000667
DELETION	SO:0000159
TRANSLOCATION	SO:0000199
INVERSION	SO:1000036
CNV	SO:0001019
DUPLICATION	SO:1000035
BREAKEND	NA
SYMBOLIC	NA

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