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mApoSyl1.1

Organism name:
Apodemus sylvaticus (European woodmouse)
BioSample:
SAMEA7702024
BioProject:
PRJEB56948
Submitter:
WELLCOME SANGER INSTITUTE
Date:
2022/10/28
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_947179515.1 (latest)
RefSeq assembly accession:
GCF_947179515.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT
  • Data displayed for RefSeq version
WGS Project:
CAMXCG01
Assembly method:
various
Genome coverage:
25x
Sequencing technology:
PacBio,Illumina,Arima2
Linked assembly:
GCA_947179525.1 (alternate pseudohaplotype of diploid)

IDs: 14246201 [UID] 37011728 [GenBank] 37302078 [RefSeq]

See Genome Information for Apodemus sylvaticus

Pathogen Detection Resources

There are 3 assemblies for this organism

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History (Show revision history)

Comment

The assembly mApoSyl1.1 is based on 25x PacBio data, 10X Genomics Chromium data, and Arima2 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 gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size.  more

Global statistics

Total sequence length2,889,785,202
Total ungapped length2,889,559,585
Gaps between scaffolds0
Number of scaffolds497
Scaffold N50120,938,251
Scaffold L509
Number of contigs1,626
Contig N504,449,850
Contig L50199
Total number of chromosomes and plasmids25
Number of component sequences (WGS or clone)497

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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_947179514.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1OX359297.1=NC_067472.10
Chromosome 2OX359298.1=NC_067473.10
Chromosome 3OX359299.1=NC_067474.10
Chromosome 4OX359300.1=NC_067475.10
Chromosome 5OX359301.1=NC_067476.11
Chromosome 6OX359303.1=NC_067477.10
Chromosome 7OX359304.1=NC_067478.10
Chromosome 8OX359305.1=NC_067479.10
Chromosome 9OX359306.1=NC_067480.10
Chromosome 10OX359307.1=NC_067481.10
Chromosome 11OX359308.1=NC_067482.10
Chromosome 12OX359309.1=NC_067483.10
Chromosome 13OX359310.1=NC_067484.10
Chromosome 14OX359311.1=NC_067485.10
Chromosome 15OX359312.1=NC_067486.11
Chromosome 16OX359313.1=NC_067487.10
Chromosome 17OX359314.1=NC_067488.10
Chromosome 18OX359315.1=NC_067489.10
Chromosome 19OX359316.1=NC_067490.10
Chromosome 20OX359317.1=NC_067491.10
Chromosome 21OX359318.1=NC_067492.10
Chromosome 22OX359319.1=NC_067493.10
Chromosome 23OX359320.1=NC_067494.10
Chromosome XOX359302.1=NC_067495.10
Chromosome YOX359321.1=NC_067496.19
unplacedn/an/an/a461

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule2,889,785,2024972,889,559,585120,938,2511,1290
Chromosome 1Assembled molecule211,764,3361211,747,136211,764,336860
Chromosome 2Assembled molecule188,060,7991188,049,999188,060,799540
Chromosome 3Assembled molecule171,660,3621171,654,745171,660,362290
Chromosome 4Assembled molecule170,262,5241170,251,324170,262,524560
Chromosome 5AllAssembled moleculeUnlocalized scaffolds165,766,004165,109,893656,111211165,757,004165,100,893656,111165,109,893165,109,893656,11145450000
Chromosome 6Assembled molecule147,565,6821147,555,682147,565,682500
Chromosome 7Assembled molecule132,812,1181132,803,318132,812,118440
Chromosome 8Assembled molecule120,938,2511120,931,251120,938,251350
Chromosome 9Assembled molecule114,967,4561114,959,856114,967,456380
Chromosome 10Assembled molecule111,231,9491111,223,949111,231,949400
Chromosome 11Assembled molecule108,324,0381108,319,238108,324,038240
Chromosome 12Assembled molecule104,471,2091104,464,009104,471,209360
Chromosome 13Assembled molecule102,393,8621102,386,462102,393,862370
Chromosome 14Assembled molecule91,741,151191,734,35191,741,151340
Chromosome 15AllAssembled moleculeUnlocalized scaffolds91,386,59089,430,6291,955,96121191,380,59089,424,6291,955,96189,430,62989,430,6291,955,96130300000
Chromosome 16Assembled molecule89,840,071189,834,87189,840,071260
Chromosome 17Assembled molecule82,792,988182,788,18882,792,988240
Chromosome 18Assembled molecule71,504,137171,498,73771,504,137270
Chromosome 19Assembled molecule68,850,066168,843,86668,850,066310
Chromosome 20Assembled molecule67,998,210167,991,21067,998,210350
Chromosome 21Assembled molecule63,776,737163,770,53763,776,737310
Chromosome 22Assembled molecule59,291,523159,284,72359,291,523340
Chromosome 23Assembled molecule57,624,522157,619,72257,624,522240
Chromosome XAssembled molecule151,773,9951151,722,195151,773,9952590
Chromosome YAllAssembled moleculeUnlocalized scaffolds15,660,8193,454,88412,205,935101915,660,8193,454,88412,205,9352,307,5013,454,8841,800,492000000
unplacedAssembled molecule127,325,803461127,325,803559,38700