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aRanTem1.1

Organism name:
Rana temporaria (common frog)
BioSample:
SAMEA7521635
BioProject:
PRJEB42171
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_905171775.1 (latest)
RefSeq assembly accession:
GCF_905171775.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT
  • Data displayed for RefSeq version
WGS Project:
CAJIMO01
Genome coverage:
63x
Linked assembly:
GCA_905171725.1 (alternate pseudohaplotype of diploid)

IDs: 9298091 [UID] 25032848 [GenBank] 25532638 [RefSeq]

See Genome Information for Rana temporaria

Pathogen Detection Resources

There are 3 assemblies for this organism

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History (Show revision history)

Comment

The assembly aRanTem1.1 is based on 63x 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 SALSA2, 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 using a genetic map provided by Dan Jeffries.  more

Global statistics

Total sequence length4,111,422,596
Total ungapped length4,085,228,578
Gaps between scaffolds0
Number of scaffolds554
Scaffold N50481,763,206
Scaffold L504
Number of contigs2,411
Contig N506,264,810
Contig L50196
Total number of chromosomes and plasmids13
Number of component sequences (WGS or clone)554

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Assembly Information

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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_905171774.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1LR991680.1=NC_053489.15
Chromosome 2LR991681.1=NC_053490.118
Chromosome 3LR991682.1=NC_053491.19
Chromosome 4LR991683.1=NC_053492.132
Chromosome 5LR991684.1=NC_053493.14
Chromosome 6LR991685.1=NC_053494.10
Chromosome 7LR991686.1=NC_053495.15
Chromosome 8LR991687.1=NC_053496.14
Chromosome 9LR991688.1=NC_053497.18
Chromosome 10LR991689.1=NC_053498.13
Chromosome 11LR991690.1=NC_053499.13
Chromosome 12LR991691.1=NC_053500.13
Chromosome 13LR991692.1=NC_053501.16
unplacedn/an/an/a441

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule4,111,422,5965544,085,228,578481,763,2061,8570
Chromosome 1AllAssembled moleculeUnlocalized scaffolds692,358,465690,654,3571,704,108615689,607,260687,903,8561,703,404690,654,357690,654,357347,7352422402000
Chromosome 2AllAssembled moleculeUnlocalized scaffolds551,203,133541,439,5719,763,56219118549,326,081539,565,9199,760,162541,439,571541,439,571594,46519618610000
Chromosome 3AllAssembled moleculeUnlocalized scaffolds497,795,133495,417,9882,377,1451019496,122,657493,745,5122,377,145495,417,988495,417,988334,6791811810000
Chromosome 4AllAssembled moleculeUnlocalized scaffolds509,869,313481,763,20628,106,10733132503,506,873477,578,41825,928,455481,763,206481,763,2061,445,44124020238000
Chromosome 5AllAssembled moleculeUnlocalized scaffolds430,400,455429,350,7201,049,735514426,691,788425,644,0261,047,762429,350,720429,350,720302,4271451414000
Chromosome 6Assembled molecule224,823,0881223,377,596224,823,0881090
Chromosome 7AllAssembled moleculeUnlocalized scaffolds213,760,996212,589,1781,171,818615211,667,045210,495,8271,171,218212,589,178212,589,178279,04199972000
Chromosome 8AllAssembled moleculeUnlocalized scaffolds191,220,154190,444,464775,690514187,256,074186,480,384775,690190,444,464190,444,464254,47490900000
Chromosome 9AllAssembled moleculeUnlocalized scaffolds187,591,228184,302,0133,289,215918187,352,642184,068,6273,284,015184,302,013184,302,013475,76211510312000
Chromosome 10AllAssembled moleculeUnlocalized scaffolds154,076,311153,779,893296,418413153,948,184153,652,266295,918153,779,893153,779,89376,9321121111000
Chromosome 11AllAssembled moleculeUnlocalized scaffolds165,063,299164,331,474731,825413164,045,563163,314,731730,832164,331,474164,331,474466,24282802000
Chromosome 12AllAssembled moleculeUnlocalized scaffolds149,101,613148,927,288174,325413148,313,293148,139,468173,825148,927,288148,927,28863,7891201191000
Chromosome 13AllAssembled moleculeUnlocalized scaffolds122,891,013121,979,656911,357716122,752,182121,841,338910,844121,979,656121,979,656185,18599972000
unplacedAssembled molecule21,268,39544121,261,34059,385270