Synteny and Rearrangement Identifier
Input whole genome alignment can be provided in SAM/BAM or in a TSV format. The columns of the TSV file are:
| Column Number | Value | Type |
|---|---|---|
| 1 | reference start position (1-based, includes start position) | int |
| 2 | reference end position (1-based, includes end position) | int |
| 3 | query start position (1-based. Includes the start position.) | int |
| 4 | query end position (1-based. Includes the end position.) | int |
| 5 | alignment length in reference | int |
| 6 | alignment length in query | int |
| 7 | alingment identity (in percent, 0-100) | float |
| 8 | alignment direction in reference (always 1) | int |
| 9 | alignment direction in query (1 for directed alignments, -1 for inverted alignments) | int |
| 10 | chromosome ID in reference | string |
| 11 | chromosome ID in query | string |
| 12 | CIGAR string corresponding to the alignment (Optional; ‘=’ for match, ‘X’ for mismatch, ‘D’ for deletion, ‘I’ for insertion) | string |
Genomes are required to be provideed in multi-fasta format. Alternatively, nucmer generated .delta file can also be provided in place of CIGAR string for SNP identification.
SyRI outputs results in TSV format and VCF file format.
| Column Number | Value | Type |
|---|---|---|
| 1 | chromosome ID in reference | string |
| 2 | reference start position (1-based, includes start position) | int |
| 3 | reference end position (1-based, includes end position) | int |
| 4 | sequence in reference (Only for SNPs and indels) | string |
| 5 | sequence in query (Only for SNPs and indels) | string |
| 6 | chromosome ID in query | string |
| 7 | query start position (1-based, includes start position) | int |
| 8 | query end position (1-based, includes end position) | int |
| 9 | unique ID (annotation type + number) | string |
| 10 | parent ID (annotation type + number) | string |
| 11 | Annotation type | string |
| 12 | Copy status (for duplications) | string |
Here, annotation type can have the following meaning:
| Annotation | Meaning | Annotation | Meaning | |
|---|---|---|---|---|
| SYN | Syntenic region | SYNAL | Alignment in syntenic region | |
| INV | Inverted region | INVAL | Alignment in inverted region | |
| TRANS | Translocated region | TRANSAL | Alignment in translocated region | |
| INVTR | Inverted translocated region | INVTRAL | Alignment in inverted translocated region | |
| DUP | Duplicated region | DUPAL | Alignment in duplicated region | |
| INVDP | Inverted duplicated region | INVDPAL | Alignment in inverted duplicated region | |
| NOTAL | Un-aligned region | SNP | Single nucleotide polymorphism | |
| CPG | Copy gain in query | CPL | Copy loss in query | |
| HDR | Highly diverged regions | TDM | Tandem repeat | |
| INS | Insertion in query | DEL | Deletion in query |
Copy status describes whether the duplicated region is in query (copygain, i.e. query has the extra copy) or in reference (copyloss, i.e. reference has the extra copy).
Parent ID corresponds to the unique ID of the annotated block (syntenic region or structural rearrangement) in which the alignment or the local variation exists. So, if there is a A->T SNP (with unique ID SNP1) in a translocated region (unique ID TRANS1) at position Chr1:10 on reference and Chr2:542 on query then the corresponding entry would be:
Chr1 10 10 A T Chr2 542 542 SNP1 TRANS1 SNP -
Above information is translated to VCF (v4.3) file format. However, since VCF is based on reference genome position, we do not output un-aligned regions in query genome in VCF file, as it was not possible to write them in context of position in reference genome.