alignment_agreement
Read-only
Read an alignment window and say how well its reads agree with the reference underneath them, the way the pileup's own bar does: the compared and differing base counts, plus the RefSeq gene models and known dbSNP variants over the same window. The reference is a FASTA in this project or a public UCSC assembly, exactly as the panel offers it. There is no threshold and no verdict: a rate in the tens of percent almost always means the reads were aligned to a different assembly than the one asked for, and when the file declares its own reference length the answer says so as a fact rather than as a judgement.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| locus | No | the window, as a locus string (`chrM:3,300-3,460`). Unset, it is the whole of the alignment's first reference — the window the panel opens on. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| variants | No | also report the known dbSNP variants in the window. Off by default, as in the panel: it is a third layer over the reads and a dense window can hold thousands. | |
| alignment | No | which BAM or SAM in this project, by name. Unset, it is the project's only alignment — and it refuses rather than guessing when there is more than one. | |
| reference | No | what to compare against: a FASTA in this project by name, or a UCSC assembly id (`hg38`, `hg19`, `mm39` — the same list the panel's picker fetches). Unset is the panel's own default, No reference, and then only the window and its annotation are reported. | |
| gene_track | No | which NCBI RefSeq set the gene models come from. Only meaningful against a UCSC assembly. The default is one curated transcript per protein-coding gene, which carries no mitochondrial genes at all — RefSeq Curated does. Values: ncbiRefSeqSelect (RefSeq Select and MANE), ncbiRefSeqCurated (RefSeq Curated), ncbiRefSeq (RefSeq All), ncbiRefSeqPredicted (RefSeq Predicted). | ncbiRefSeqSelect |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| rate | Yes | differing aligned bases as a fraction of compared ones, 0 when nothing matched up | |
| genes | Yes | the RefSeq models overlapping the window: symbol, accession, strand and bounds, as UCSC states them | |
| reads | Yes | reads read for the window | |
| noCall | Yes | aligned bases where one side is N — counted as neither, which is where this differs from an aligner's NM | |
| window | Yes | the window actually measured, as a locus string | |
| cautions | Yes | what this run earned: a reference whose length disagrees with the one the file declares, no-call bases counted as neither, and the window the numbers describe | |
| compared | Yes | aligned bases that had a reference base to compare against — the denominator | |
| variants | Yes | the dbSNP records in the window when asked for: rsID, alleles, class, highest reported frequency and ClinVar significance | |
| conclusion | Yes | the reading in one sentence, generated from this run — the panel's own words | |
| mismatched | Yes | of those, how many differ | |
| pathogenic | Yes | how many of those ClinVar calls pathogenic |