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aBufBuf1.1 alternate haplotype

Organism name:
Bufo bufo (common toad)
BioSample:
SAMEA7521636
BioProject:
PRJEB42169
Submitter:
SC
Date:
2021/01/28
Assembly type:
alternate-pseudohaplotype
Assembly level:
Scaffold
Genome representation:
full
GenBank assembly accession:
GCA_905171715.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
CAJIMM01
Genome coverage:
64x
Linked assembly:
GCA_905171765.1 (principal pseudohaplotype of diploid)

IDs: 9202591 [UID] 24782748 [GenBank]

See Genome Information for Bufo bufo

There are 2 assemblies for this organism

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History (Show revision history)

Comment

The assembly aBufBuf1.1 is based on 64x PacBio data, 10X Genomics Chromium data, BioNano data, and Arima Hi-C data generated by the Darwin Tree of Life Project (https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio ... assembly generation with Falcon-unzip, retained haplotig separation with purge_dups, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding, Hi-C based scaffolding with 3D-DNA, Arrow polishing, and two rounds of FreeBayes polishing. The mitochondrial assembly was produced at The Rockefeller University using mitoVGP. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size.  more

Global statistics

Total sequence length3,744,894,388
Total ungapped length3,744,403,109
Gaps between scaffolds0
Number of scaffolds24,195
Scaffold N50243,161
Scaffold L504,191
Number of contigs24,351
Contig N50241,528
Contig L504,231
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)24,195

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
The primary assembly unit does not have any assembled chromosomes or linkage groups.
Please download the full sequence report for information on the scaffolds.

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
unplaced3,744,894,38824,1953,744,403,109243,1611560
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