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mMusMuc1.1

Organism name:
Mus musculus (house mouse)
BioSample:
SAMEA112251260
BioProject:
PRJEB60144
Submitter:
WELLCOME SANGER INSTITUTE
Date:
2023/04/08
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_949316315.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
CASGGP01
Assembly method:
various
Genome coverage:
34x
Sequencing technology:
PacBio,OmniC
Linked assembly:
GCA_949316305.1 (alternate pseudohaplotype of diploid)

IDs: 16568611 [UID] 42617258 [GenBank]

See Genome Information for Mus musculus

Pathogen Detection Resources

There are 65 assemblies for this organism

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History (Show revision history)

Comment

The assembly mMusMuc1.1 is based on 34x PacBio data and OmniC 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 Hifiasm, retained haplotig separation ... with purge_dups, and Hi-C based scaffolding with YaHS. The mitochondrial genome was assembled using MitoHiFi. Finally, the primary assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds are named by synteny based on Mus musculus (house mouse) GCA_001632555.1.  more

Global statistics

Total sequence length2,770,968,735
Total ungapped length2,770,948,535
Gaps between scaffolds0
Number of scaffolds179
Scaffold N50132,150,484
Scaffold L509
Number of contigs280
Contig N5039,533,248
Contig L5023
Total number of chromosomes and plasmids21
Number of component sequences (WGS or clone)179

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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
non-nuclear
Assembly Unit: Primary Assembly (GCA_949316314.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1OX439014.1n/an/a0
Chromosome 2OX439015.1n/an/a0
Chromosome 3OX439017.1n/an/a0
Chromosome 4OX439018.1n/an/a0
Chromosome 5OX439019.1n/an/a1
Chromosome 6OX439020.1n/an/a0
Chromosome 7OX439021.1n/an/a0
Chromosome 8OX439023.1n/an/a0
Chromosome 9OX439025.1n/an/a0
Chromosome 10OX439022.1n/an/a0
Chromosome 11OX439024.1n/an/a0
Chromosome 12OX439027.1n/an/a0
Chromosome 13OX439026.1n/an/a0
Chromosome 14OX439028.1n/an/a0
Chromosome 15OX439029.1n/an/a0
Chromosome 16OX439031.1n/an/a0
Chromosome 17OX439030.1n/an/a2
Chromosome 18OX439032.1n/an/a0
Chromosome 19OX439033.1n/an/a0
Chromosome XOX439016.1n/an/a0
unplacedn/an/an/a155

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule2,770,952,4361782,770,932,236132,150,4841010
Chromosome 1Assembled molecule200,127,2701200,125,470200,127,27090
Chromosome 2Assembled molecule184,589,6121184,588,612184,589,61250
Chromosome 3Assembled molecule166,580,4771166,579,477166,580,47750
Chromosome 4Assembled molecule165,824,8771165,823,077165,824,87790
Chromosome 5AllAssembled moleculeUnlocalized scaffolds152,368,106151,737,448630,658211152,367,706151,737,048630,658151,737,448151,737,448630,658220000
Chromosome 6Assembled molecule151,648,8691151,647,069151,648,86990
Chromosome 7Assembled molecule146,218,8371146,217,037146,218,83790
Chromosome 8Assembled molecule129,827,2421129,826,042129,827,24260
Chromosome 9Assembled molecule129,049,9391129,049,139129,049,93940
Chromosome 10Assembled molecule132,150,4841132,149,284132,150,48460
Chromosome 11Assembled molecule129,618,5811129,618,181129,618,58120
Chromosome 12Assembled molecule119,923,7331119,923,133119,923,73330
Chromosome 13Assembled molecule126,876,4551126,875,855126,876,45530
Chromosome 14Assembled molecule119,895,5601119,893,560119,895,560100
Chromosome 15Assembled molecule101,857,3621101,856,962101,857,36220
Chromosome 16Assembled molecule96,079,412196,078,81296,079,41230
Chromosome 17AllAssembled moleculeUnlocalized scaffolds98,020,79697,324,981695,81531298,020,39697,324,581695,81597,324,98197,324,981528,489220000
Chromosome 18Assembled molecule89,877,872189,877,27289,877,87230
Chromosome 19Assembled molecule59,470,459159,470,05959,470,45920
Chromosome XAssembled molecule168,231,5391168,230,139168,231,53970
unplacedAssembled molecule102,714,954155102,714,9542,041,00000
MoleculeTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
Mitochondrion MT16,299116,29916,29900