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aBufBuf1.1

Organism name:
Bufo bufo (common toad)
BioSample:
SAMEA7521636
BioProject:
PRJEB42168
Submitter:
Wellcome Sanger Institute
Date:
2021/01/28
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_905171765.1 (latest)
RefSeq assembly accession:
GCF_905171765.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT (in non-nuclear assembly-unit)
  • Data displayed for RefSeq version
WGS Project:
CAJIMN01
Genome coverage:
64x
Linked assembly:
GCA_905171715.1 (alternate pseudohaplotype of diploid)

IDs: 9298081 [UID] 25032778 [GenBank] 25500478 [RefSeq]

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 length5,044,744,194
Total ungapped length5,034,865,963
Gaps between scaffolds0
Number of scaffolds1,306
Scaffold N50635,713,434
Scaffold L504
Number of contigs5,501
Contig N503,959,750
Contig L50350
Total number of chromosomes and plasmids11
Number of component sequences (WGS or clone)1,306

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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
Assembly Unit: Primary Assembly (GCF_905171764.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1LR991667.1=NC_053389.19
Chromosome 2LR991668.1=NC_053390.114
Chromosome 3LR991669.1=NC_053391.15
Chromosome 4LR991670.1=NC_053392.18
Chromosome 5LR991671.1=NC_053393.11
Chromosome 6LR991672.1=NC_053394.13
Chromosome 7LR991673.1=NC_053395.16
Chromosome 8LR991674.1=NC_053396.15
Chromosome 9LR991675.1=NC_053397.10
Chromosome 10LR991676.1=NC_053398.12
Chromosome 11LR991677.1=NC_053399.12
unplacedn/an/an/a1,240

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule5,044,744,1941,3065,034,865,963635,713,4344,1950
Chromosome 1AllAssembled moleculeUnlocalized scaffolds845,527,104843,366,1802,160,9241019843,021,832840,861,0082,160,824843,366,180843,366,1801,130,4387667651000
Chromosome 2AllAssembled moleculeUnlocalized scaffolds843,777,746842,558,4041,219,34215114842,429,378841,210,1361,219,242842,558,404842,558,40484,5016366351000
Chromosome 3AllAssembled moleculeUnlocalized scaffolds708,853,718707,956,555897,163615708,043,729707,146,666897,063707,956,555707,956,555454,4795485471000
Chromosome 4AllAssembled moleculeUnlocalized scaffolds636,938,567635,713,4341,225,133918635,868,632634,643,5121,225,120635,713,434635,713,434174,8734464451000
Chromosome 5AllAssembled moleculeUnlocalized scaffolds567,337,959567,300,18237,777211566,229,757566,191,98037,777567,300,182567,300,18237,7774474470000
Chromosome 6AllAssembled moleculeUnlocalized scaffolds440,511,168439,630,435880,733413439,289,201438,514,866774,335439,630,435439,630,435514,9464344313000
Chromosome 7AllAssembled moleculeUnlocalized scaffolds237,626,771236,595,4451,031,326716237,173,839236,142,5131,031,326236,595,445236,595,445183,7442192190000
Chromosome 8AllAssembled moleculeUnlocalized scaffolds232,832,085231,667,8221,164,263615232,308,758231,144,4951,164,263231,667,822231,667,822412,5653313310000
Chromosome 9Assembled molecule230,778,8671230,269,848230,778,8671340
Chromosome 10AllAssembled moleculeUnlocalized scaffolds151,721,754151,572,763148,991312151,639,131151,490,140148,991151,572,763151,572,76396,8591001000000
Chromosome 11AllAssembled moleculeUnlocalized scaffolds103,708,139103,205,957502,182312103,665,844103,163,762502,082103,205,957103,205,957276,41282811000
unplacedAssembled molecule45,130,3161,24044,926,01443,778520
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