Mapped sequence: 653,124,558bp; Unmapped sequence: 71,126,376bp.
Retrieve the FASTA sequence: xma_washu_4.4.2-jhp_0.1.fa
Unplaced scaffolds: xma_washu_4.4.2-unplaced.fa
Genome AGP definition for scaffolds: xma_washu_4.4.2-jhp_0.1.agp
Genome AGP definition for chromosomes: xma_washu_4.4.2-jhp_0.1.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 |
14391 total markers mapped; 1794 conflicting markers excluded. 101 scaffolds mapped to multiple linkage groups. 231 scaffolds were split: 2 fragments: 163 cases 3 fragments: 44 cases 4 fragments: 16 cases 5 fragments: 2 cases 6 fragments: 4 cases 7 fragments: 2 cases 2288 total scaffolds mapped from 1950 original scaffolds. 653,124,558bp total length.
These scaffolds appear to be misassembled, however markers were in conflict when a split was attempted.
Genes were taken from the Walter transcriptome, version 4
(file Xm_txm4.cds_blastn_filtered.ENSG.fasta
) using all
velvet/oasis transcripts that contain at least one BLAST hit to another teleost
species. These genes were then aligned to the WashU_4.4.2-JHP_0.1
reference genome using BLAT, requiring that 95% of the transcript
align with 95% identitiy. All transcripts for a particular gene were
aligned and the longest alignment was then used as the start/end
coordinates for the gene model.
26,934 gene models; 39,835 transcripts.