Angel Amores, Julian Catchen, Indrajit Nanda, Wesley Warren, Ron Walter, Manfred Schartl, and John Postlethwait. A RAD-tag Genetic Map for the Platyfish (Xiphophorus maculatus) Reveals Mechanisms of Karyotype Evolution Among Teleost Fish. Genetics, 197:2, 625-641. [reprint]
Mapped sequence: 653,641,933bp; Unmapped sequence: 71,161,821bp.
Retrieve the FASTA sequence: xma_washu_4.4.2-jhp_1.0.fa
Unplaced scaffolds: xma_washu_4.4.2-jhp_1.0.unplaced_scaffolds.fa
Genome AGP definition for scaffolds:
xma_washu_4.4.2-jhp_1.0.agp
Genome AGP definition for chromosomes:
xma_washu_4.4.2-jhp_1.0.flat.agp
| LG1 | LG5 | LG9 | LG13 | LG17 | LG21 |
| LG2 | LG6 | LG10 | LG14 | LG18 | LG22 |
| LG3 | LG7 | LG11 | LG15 | LG19 | LG23 |
| LG4 | LG8 | LG12 | LG16 | LG20 | LG24 |
15292 total markers mapped; 770 conflicting markers excluded. 102 scaffolds mapped to multiple linkage groups. 212 scaffolds were split: 2 fragments: 139 cases 3 fragments: 43 cases 4 fragments: 22 cases 5 fragments: 5 cases 6 fragments: 2 cases 7 fragments: 1 cases 2271 total scaffolds mapped from 1944 original scaffolds. 653,417,233bp total length.
These scaffolds appear to be misassembled, however markers were in conflict when a split was attempted.
| Scaffolds split across linkage groups | Scaffolds split within a linkage group |
|---|---|
|
JH556770.1 JH556689.1 JH557978.1 JH557060.1 |
JH556666.1 [markers overlap] JH556815.1 [markers overlap] JH556723.1 [too many markers at node 207] JH556705.1 [markers overlap] JH556673.1 [markers overlap] JH556672.1 [markers overlap] JH558760.1 [too many 'start' or 'end' markers at node 0] JH556715.1 [markers overlap] JH556938.1 [too many 'start' or 'end' markers at node 149] JHP00225.0 [markers overlap] JH556875.1 [markers overlap] JHP00066.0 [markers overlap] |
Genes were downloaded from Ensembl release 76 and their coordinates were translated to this chromosome assembly.
Processed 20,742 genes; 20,660 translated 82 failures (26 on multiple chromosomes). 37 genes on 1 mising scaffold (NC_011379) Processed 520,477 GTF components: 493,546 translations 122 translation errors 26,701 components on unassembled scaffolds (no translation necessary) 108 components in 1 missing scaffolds.