Alignment Data Model Schema

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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Alignment Data Model Schema