Pseudomolecule to Parts Coordinates

The following coordinates used in the "From" field domonstrate the types of input accepted for converting coordinates from the full-length pseudomolecule coordinates to the "parts" coordinates:

• Coordinates contained within part1: chr4D:1-100
• Coordinates contained within part2: chr4D:500000000-550000000
• Coordinates with thousand separator: chr4D:500,000,000-550,000,000
• Coordinates with alternative range separator: chr4D:1..100
• Coordinates with spaces seperating values: chr4D 1 100
• Coordinates with tabs seperating values (enables copy-and-paste from Excel): chr4D 1 100
• Case insensitive: ChR4d:1-100
• Coordinates without "chr" prefix: 4D:1-100
• Single point coordinate: chr4D:500000000

Parts to Pseudomolecule Coordinates

The following coordinates used in the "From" field domonstrate the types of input accepted for converting coordinates from the "parts" coordinates to the full-length pseudomolecule coordinates:

• Coordinates from part1: chr4D_part1:1-100
• Coordinates from part2: chr4D_part2:48995380-98995380
• Coordinates with thousand separator: chr4D_part1:100,000,000-100,500,000
• Coordinates with alternative range separator: chr4D_part1:1..100
• Coordinates with spaces seperating values: chr4D_part1 1 100
• Coordinates with tabs seperating values (enables copy-and-paste from Excel): chr4D_part1 1 100
• Case insensitive: ChR4d_PaRt1:1-100
• Coordinates without "chr" prefix: 4D_part1:1-100
• Single point coordinate: chr4D_part2:48995380

The "From" field accepts coordinates in the form of chr_id:bp_coord. Where:

• Chromosome ID (chr_id) can be either a full pseudomolecule ID (e.g. chr1D) or a part chromosome ID (e.g. chr5B_part1)
• Coordinates (bp_coord) is a range in the form of from_bp-to_bp. The range separator can one or more hyphens (e.g. -) or two or more dots (e.g. ..). The from_bp and to_bp values must be numeric but may contain commas (thousand separators). If from_bp is greater than to_bp, their values are swapped for the purpose of the conversion (e.g. chr1D:200,000-1,000)

This page also accepts a coordinate via URL parameters. Simply add something like "?from=chr7D:1000-2000" to the URL e.g. http://crobiad.agwine.adelaide.edu.au/dawn/coord/?from=chr7D:1000-2000

When the IWGSC released the Chinese spring RefSeq v1.0 genome assembly there were many commonly used bioinformatics tools incapable of dealing with pseudomolecules longer than ~537 Mbp. More specifically, the BAI index file which provides rapid data extraction from BAM (NGS read alignments), tabix indexed VCF (SNP/structural variants) and tabix index GFF3 (gene annotations) files does not support reference sequences longer than 2²⁹-1 bp (~537 Mbp).

As a work-around to this technical limitation, the IWGSC split each pseudomolecule into 2 parts. The fisrt part containing the short arm, centromere and start of the long arm. The second part containing the remainder of the long arm. DAWN currently uses the "2-part" version of the IWGSC RefSeq v1.0 in order to be able to show read alignments, variants and gene features directly from their source files.

This coordinate converter is capable of converting genome coordinates between both the "2-part" and the full-length pseudomolecules versions of the IWGSC RefSeq v1.0 genome assembly.

The following table shows the bp location of where the pseudomolecule splits are found:

Chromosome	Split After (bp)
chr1A	471,304,005
chr1B	438,720,154
chr1D	452,179,604
chr2A	462,376,173
chr2B	453,218,924
chr2D	462,216,879
chr3A	454,103,970
chr3B	448,155,269
chr3D	476,235,359
chr4A	452,555,092
chr4B	451,014,251
chr4D	451,004,620
chr5A	453,230,519
chr5B	451,372,872
chr5D	451,901,030
chr6A	452,440,856
chr6B	452,077,197
chr6D	450,509,124
chr7A	450,046,986
chr7B	453,822,637
chr7D	453,812,268
chrUn	480,980,714