Xiphophorus maculatus Genome Assembly

WashU Genome Assembly version 4.4.2; JHP Genetic Map Assembly 0.1

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

View the assembly logs:

LG1	LG5	LG9	LG13	LG17	LG21
LG2	LG6	LG10	LG14	LG18	LG22
LG3	LG7	LG11	LG15	LG19	LG23
LG4	LG8	LG12	LG16	LG20	LG24

Assembly Statistics:

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.

Problem Scaffolds

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
JH556677.1 JH556753.1 JH556755.1 JH556972.1 JH556667.1 JH556770.1 JH557114.1 JH556863.1 JH557164.1 JH556754.1 JH556813.1 JH556661.1 JH556751.1 JH556922.1 JH556689.1 JH556761.1 JH557978.1 JH557060.1 JH556716.1 JH556886.1 JH557025.1 JH556780.1	JH556746.1 JH556787.1 JH556713.1 JH556684.1 JHP00099.0 JHP00020.0 JH556666.1 JH556815.1 JH556705.1 JH556753.1 JH556672.1 JH557734.1 JH556745.1 JH557424.1 JH558760.1 JH557156.1 JH557369.1 JH556765.1 JH557015.1 JH558121.1 JHP00064.0 JH556717.1 JH556938.1 JH556838.1 JH556846.1 JHP00167.0 JH557016.1 JH556793.1 JH557033.1 JH556699.1 JHP00053.0 JH556875.1 JHP00124.0 JHP00039.0 JH556932.1

Gene Models

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.

Gene model locations: xma_summary.tsv
cDNA sequence of gene transcripts: xma_cdna.fa
A key mapping locus/transcript names from Walter Transcriptome to WashU_4.4.2-JHP-0.1 gene model names: xma_key.tsv