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mLoxAfr1.hap2

Organism name:
Loxodonta africana (African savanna elephant)
Isolate:
mLoxAfr1
Sex:
male
BioSample:
SAMN32756554
BioProject:
PRJNA924322
Submitter:
Vertebrate Genomes Project
Date:
2023/05/16
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_030014295.1 (latest)
RefSeq assembly accession:
GCF_030014295.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Different: number of assembly-units
  • Data displayed for RefSeq version
WGS Project:
JASCQR01
Assembly method:
Hifiasm + Hi-C phasing v. 0.16.1 + galaxy3; Bionano Solve v. 3.7; yahs v. 1.2a.2 + galaxy0
Expected final version:
no
Genome coverage:
43.0x
Sequencing technology:
PacBio Sequel II HiFi; Bionano DLS; Arima Hi-C v2

IDs: 16599661 [UID] 42703568 [GenBank] 55616348 [RefSeq]

See Genome Information for Loxodonta africana

Pathogen Detection Resources

There are 10 assemblies for this organism

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History (Show revision history)

Comment

Global statistics

Total sequence length3,540,876,381
Total ungapped length3,537,187,813
Gaps between scaffolds0
Number of scaffolds879
Scaffold N50119,600,562
Scaffold L5011
Number of contigs1,110
Contig N5082,653,632
Contig L5015
Total number of chromosomes and plasmids29
Number of component sequences (WGS or clone)879

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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_030015425.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM057419.1=NC_087342.10
Chromosome 2CM057420.1=NC_087343.16
Chromosome 3CM057421.1=NC_087344.10
Chromosome 4CM057422.1=NC_087345.10
Chromosome 5CM057423.1=NC_087346.10
Chromosome 6CM057424.1=NC_087347.10
Chromosome 7CM057425.1=NC_087348.10
Chromosome 8CM057426.1=NC_087349.10
Chromosome 9CM057427.1=NC_087350.10
Chromosome 10CM057428.1=NC_087351.11
Chromosome 11CM057429.1=NC_087352.10
Chromosome 12CM057430.1=NC_087353.10
Chromosome 13CM057431.1=NC_087354.11
Chromosome 14CM057432.1=NC_087355.13
Chromosome 15CM057433.1=NC_087356.10
Chromosome 16CM057434.1=NC_087357.10
Chromosome 17CM057435.1=NC_087358.10
Chromosome 18CM057436.1=NC_087359.10
Chromosome 19CM057437.1=NC_087360.11
Chromosome 20CM057438.1=NC_087361.10
Chromosome 21CM057439.1=NC_087362.10
Chromosome 22CM057440.1=NC_087363.12
Chromosome 23CM057441.1=NC_087364.10
Chromosome 24CM057442.1=NC_087365.12
Chromosome 25CM057443.1=NC_087366.10
Chromosome 26CM057444.1=NC_087367.19
Chromosome 27CM057445.1=NC_087368.13
Chromosome XCM057446.1=NC_087369.11
Chromosome YCM057447.1=NC_087370.116
unplacedn/an/an/a805

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule3,540,876,3818793,537,187,813119,600,5622310
Chromosome 1Assembled molecule241,857,1371241,851,965241,857,13770
Chromosome 2AllAssembled moleculeUnlocalized scaffolds237,903,004233,670,2084,232,796716237,900,557233,667,7614,232,796233,670,208233,670,2081,146,817220000
Chromosome 3Assembled molecule214,621,6981214,186,084214,621,698160
Chromosome 4Assembled molecule193,759,6191193,759,180193,759,61950
Chromosome 5Assembled molecule163,053,4351163,053,435163,053,43500
Chromosome 6Assembled molecule141,835,2631141,835,037141,835,26330
Chromosome 7Assembled molecule136,918,4611136,900,385136,918,461120
Chromosome 8Assembled molecule135,789,6351135,788,835135,789,63540
Chromosome 9Assembled molecule124,161,9181124,067,312124,161,91830
Chromosome 10AllAssembled moleculeUnlocalized scaffolds120,854,388119,600,5621,253,826211120,853,575119,599,7491,253,826119,600,562119,600,5621,253,826550000
Chromosome 11Assembled molecule109,346,7011109,337,718109,346,70130
Chromosome 12Assembled molecule106,945,0071106,934,999106,945,00740
Chromosome 13AllAssembled moleculeUnlocalized scaffolds98,218,13196,742,5631,475,56821198,174,46396,698,9081,475,55596,742,56396,742,5631,475,568871000
Chromosome 14AllAssembled moleculeUnlocalized scaffolds98,121,74993,128,2994,993,45041398,121,51093,128,0864,993,42493,128,29993,128,2991,662,510422000
Chromosome 15Assembled molecule87,036,990187,036,56487,036,99040
Chromosome 16Assembled molecule85,807,135185,806,90985,807,13530
Chromosome 17Assembled molecule84,112,027184,108,33784,112,02720
Chromosome 18Assembled molecule83,753,080183,752,48083,753,08030
Chromosome 19AllAssembled moleculeUnlocalized scaffolds83,300,34081,981,3211,319,01921183,299,14081,980,1211,319,01981,981,32181,981,3211,319,019660000
Chromosome 20Assembled molecule82,234,945182,191,73682,234,94570
Chromosome 21Assembled molecule80,486,019180,484,44080,486,01960
Chromosome 22AllAssembled moleculeUnlocalized scaffolds80,162,93577,113,1503,049,78531280,153,36677,103,5813,049,78577,113,15077,113,1502,731,403110000
Chromosome 23Assembled molecule77,535,617177,535,35777,535,61740
Chromosome 24AllAssembled moleculeUnlocalized scaffolds66,867,53265,527,6661,339,86631266,867,13265,527,2661,339,86665,527,66665,527,666741,517220000
Chromosome 25Assembled molecule65,798,596165,798,19665,798,59620
Chromosome 26AllAssembled moleculeUnlocalized scaffolds64,006,26950,538,04313,468,226101964,005,21750,537,03013,468,18750,538,04350,538,0432,249,406963000
Chromosome 27AllAssembled moleculeUnlocalized scaffolds40,140,45738,945,1411,195,31641338,597,84837,402,5321,195,31638,945,14138,945,141639,50110100000
Chromosome XAllAssembled moleculeUnlocalized scaffolds178,965,324178,713,466251,858211178,936,638178,684,980251,658178,713,466178,713,466251,85824231000
Chromosome YAllAssembled moleculeUnlocalized scaffolds38,054,11426,937,37211,116,7421711638,005,08626,893,25911,111,82726,937,37226,937,372772,472981000
unplacedAssembled molecule219,228,855805217,844,312634,081630