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| string | sequence = 1 |
| | The sequence that has been aligned. More...
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| Path | path = 2 |
| | The Path that the sequence follows in the graph it has been aligned to, containing the Edits that modify the graph to produce the sequence. More...
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| string | name = 3 |
| | The name of the sequence that has been aligned. Similar to read name in BAM. More...
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| bytes | quality = 4 |
| | The quality scores for the sequence, as values on a 0-255 scale. More...
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| int32 | mapping_quality = 5 |
| | The mapping quality score for the alignment, in Phreds. More...
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| int32 | score = 6 |
| | The score for the alignment, in points. More...
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| int32 | query_position = 7 |
| | The offset in the query at which this Alignment occurs. More...
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| | reserved |
| | Old field 8 has been removed. More...
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| string | sample_name = 9 |
| | The name of the sample that produced the aligned read. More...
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| string | read_group = 10 |
| | The name of the read group to which the aligned read belongs. More...
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| Alignment | fragment_prev = 11 |
| | The previous Alignment in the fragment. Contains just enough information to locate the full Alignment; e.g. contains an Alignment with only a name, or only a graph mapping position. More...
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| Alignment | fragment_next = 12 |
| | Similarly, the next Alignment in the fragment. More...
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| bool | is_secondary = 15 |
| | Flag marking the Alignment as secondary. All but one maximal-scoring alignment of a given read in a GAM file must be secondary. More...
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| double | identity = 16 |
| | Portion of aligned bases that are perfect matches, or 0 if no bases are aligned. More...
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| repeated< Path > | fragment = 17 |
| | An estimate of the length of the fragment, if this Alignment is paired. More...
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| repeated< Locus > | locus = 18 |
| | The loci that this alignment supports. TODO: get rid of this, we have annotations in our data model again. More...
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| repeated< Position > | refpos = 19 |
| | Position of the alignment in reference paths embedded in graph. Each position has a path name, and the Alignment's minimum position along the path as an offset. More...
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| bool | read_paired = 20 |
| | SAMTools-style flags. More...
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| bool | read_mapped = 21 |
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| bool | mate_unmapped = 22 |
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| bool | read_on_reverse_strand = 23 |
| |
| bool | mate_on_reverse_strand = 24 |
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| bool | soft_clipped = 25 |
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| bool | discordant_insert_size = 26 |
| |
| double | uniqueness = 27 |
| | The fraction of bases in the alignment that are covered by MEMs with <=1 total hits in the graph. More...
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| double | correct = 28 |
| | Correctness metric 1 = perfectly aligned to truth, 0 = not overlapping true alignment. More...
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| repeated< int32 > | secondary_score = 29 |
| | The ordered list of scores of secondary mappings. More...
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| double | fragment_score = 30 |
| | Score under the given fragment model, assume higher is better. More...
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| bool | mate_mapped_to_disjoint_subgraph = 31 |
| |
| string | fragment_length_distribution = 32 |
| | The fragment length distribution under which a paired-end alignment was aligned. More...
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| reserved | to |
| | Haplotype-scoring-related fields migrated to the annotation system. More...
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| double | time_used = 35 |
| | The time this alignment took. More...
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| Position | to_correct = 36 |
| | A path/offset/orientation pair specifying the distance to the correct alignment. More...
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| bool | correctly_mapped = 37 |
| | This can be set to true to annotate the Alignment as having been mapped correctly. More...
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| google protobuf Struct | annotation = 100 |
| | Annotations carried along with the Alignment. More...
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Alignments link query strings, such as other genomes or reads, to Paths.
