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mArvNil1.pat.X

Organism name:
Arvicanthis niloticus (Nile rat)
Isolate:
mArvNil1
Sex:
male
BioSample:
SAMN12611849
BioProject:
PRJNA608735
Submitter:
Vertebrate Genomes Project
Date:
2020/03/27
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_011762505.1 (latest)
RefSeq assembly accession:
GCF_011762505.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT
  • Data displayed for RefSeq version
WGS Project:
JAAOMG01
Assembly method:
TrioCanu v. 1.8; purge_dups v. 1.0.0; Scaff 10x v. 4.1.0; Bionano solve v. 3.2.1_04122018; Salsa2 HiC v. 2.2; Arrow polishing and gap filling v. smrtlink_6.0.0.47841; Freebayes v. 1.3.1; gEVAL manual curation v. 2020-01-16; VGP trio assembly pipeline v. 1.6
Expected final version:
no
Genome coverage:
60.95x
Sequencing technology:
PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS

IDs: 6463581 [UID] 18124138 [GenBank] 19562748 [RefSeq]

See Genome Information for Arvicanthis niloticus

Pathogen Detection Resources

There are 4 assemblies for this organism

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History (Show revision history)

Comment

This is the trio assembly merged haplotype data. The maternal and paternal haplotype sequences are in WGS projects JAAOME000000000 and JAAOMF000000000 respectively.

Global statistics

Total sequence length2,496,761,438
Total ungapped length2,476,471,911
Gaps between scaffolds0
Number of scaffolds1,595
Scaffold N5082,689,117
Scaffold L5011
Number of contigs3,219
Contig N5011,143,170
Contig L5056
Total number of chromosomes and plasmids23
Number of component sequences (WGS or clone)1,595

Supplemental Content

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Assembly Information

Related Information

PubMed articles for this assembly

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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_011762575.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM022251.1=NC_047658.10
Chromosome 2CM022252.1=NC_047659.10
Chromosome 3CM022253.1=NC_047660.10
Chromosome 4CM022254.1=NC_047661.10
Chromosome 5CM022255.1=NC_047662.10
Chromosome 6CM022256.1=NC_047663.10
Chromosome 7CM022257.1=NC_047664.10
Chromosome 8CM022258.1=NC_047665.10
Chromosome 9CM022259.1=NC_047666.10
Chromosome 10CM022260.1=NC_047667.10
Chromosome 11CM022261.1=NC_047668.10
Chromosome 12CM022262.1=NC_047669.10
Chromosome 13CM022263.1=NC_047670.10
Chromosome 14CM022264.1=NC_047671.10
Chromosome 15CM022265.1=NC_047672.10
Chromosome 16CM022266.1=NC_047673.10
Chromosome 17CM022267.1=NC_047674.10
Chromosome 18CM022268.1=NC_047675.10
Chromosome 19CM022269.1=NC_047676.10
Chromosome 20CM022270.1=NC_047677.10
Chromosome 21CM022271.1=NC_047678.10
Chromosome XCM022272.1=NC_047679.10
Chromosome Yn/an/an/a4
unplacedn/an/an/a1,569

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule2,496,761,4381,5952,476,471,91182,689,1171,6240
Chromosome 1Assembled molecule167,116,5631166,495,568167,116,563500
Chromosome 2Assembled molecule149,323,6081148,696,984149,323,608610
Chromosome 3Assembled molecule139,271,5911139,166,373139,271,591400
Chromosome 4Assembled molecule135,118,0991133,971,227135,118,099610
Chromosome 5Assembled molecule108,691,0401108,572,899108,691,040370
Chromosome 6Assembled molecule108,648,0011107,798,470108,648,001230
Chromosome 7Assembled molecule91,426,705191,072,10091,426,705560
Chromosome 8Assembled molecule88,234,701188,186,52488,234,701460
Chromosome 9Assembled molecule86,386,494186,246,29286,386,494510
Chromosome 10Assembled molecule82,689,117182,643,83182,689,117250
Chromosome 11Assembled molecule80,941,235180,787,71080,941,235380
Chromosome 12Assembled molecule79,553,684178,845,34179,553,684820
Chromosome 13Assembled molecule78,041,482177,846,84078,041,482390
Chromosome 14Assembled molecule76,397,992176,397,67976,397,99240
Chromosome 15Assembled molecule73,895,232173,195,40673,895,232440
Chromosome 16Assembled molecule73,423,486172,510,64673,423,486250
Chromosome 17Assembled molecule64,041,812163,790,31264,041,812180
Chromosome 18Assembled molecule54,839,141154,838,62854,839,14150
Chromosome 19Assembled molecule53,135,676152,795,61053,135,676770
Chromosome 20Assembled molecule52,431,192152,370,88152,431,192270
Chromosome 21Assembled molecule52,083,330151,538,75652,083,330510
Chromosome XAssembled molecule130,353,3351127,729,636130,353,3351190
Chromosome YAllAssembled moleculeUnlocalized scaffolds29,816,896029,816,89640425,657,120025,657,1206,376,36306,376,3631060106000
unplacedAssembled molecule440,901,0261,569435,317,07840,139,7545390