The following table is a quick cheat sheet identifying the genomic coordinate conventions used at different sites, file formats, etc. I welcome corrections and additions in the comments. I'll add them to the companion sheet as time allows.
A more detailed description of genome coordinate systems can be found in my earlier post. Note that in this table, I consider zero-based, half-open coordinate conventions to be equivalent to space-counted, zero-start and so do not distinguish them in the table.
Special thanks to John DiCarlo's insights and suggestions!
A more detailed description of genome coordinate systems can be found in my earlier post. Note that in this table, I consider zero-based, half-open coordinate conventions to be equivalent to space-counted, zero-start and so do not distinguish them in the table.
| Name | Resource Type | Chromosome | 0 vs 1 | Space vs Base | Notes |
|---|---|---|---|---|---|
| UCSC Genome Browser | Genome Browser | chr1, chr2, .. chrX, chrY, chrM | 1 | Base | Note that when zooming in on the genome browser, the positioning of the tick marks appears to use a space-counted, 0-start convention. As discussed here, this is not the intention. To get the 1-based position, the base coordinate corresponds to the tick mark to its immediate right. |
| NCBI Map Viewer | Genome Browser | 1, 2, .. X, Y, MT | 1 | Base | |
| Ensembl Location Viewer | Genome Browser | 1, 2, .. X, Y, MT | 1 | Base | |
| UCSC BLAT | Web Tool | chr1, chr2, .. chrX, chrY, chrM | 1 | Base | |
| NCBI BLAST | Web Tool | chr1, chr2, .. chrX, chrY, chrMT | 1 | Base | |
| UCSC Table Browser | Web Tool | chr1, chr2, .. chrX, chrY, chrM | 0 | Space | Output formats are all 0-space formats. However, when specifying the region field is 1-base format. |
| BED Format | File Format | chr1, chr2, .. chrX, chrY, chrM | 0 | Space | |
| WIG Format | File Format | chr1, chr2, .. chrX, chrY, chrM | 1 | Base | UCSC's Wiggle Track Format |
| Galaxy Interval Format | File Format | chr1, chr2, .. chrX, chrY, chrM | 0 | Space | |
| GFF/GTF/GFF3 Format | File Format | Depends on context | 1 | Base | Chromosome names depend on resource using the file format |
| VCF Format | File Format | Depends on context | 1 | Base | Chromosome just needs to refer to an identifier in a reference genome or can be a contig id. Position 0 and N+1 (where N = chrom length) are used to refer to telomeres. |
| UCSC Annotation Files | Data File | chr1, chr2, .. chrX, chrY, chrM | 0 | Space |