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ilManJurt1.1

Organism name:
Maniola jurtina (meadow brown)
BioSample:
SAMEA7523158
BioProject:
PRJEB43489
Submitter:
WELLCOME SANGER INSTITUTE
Date:
2021/03/19
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_905333055.1 (latest)
RefSeq assembly accession:
GCF_905333055.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT
  • Data displayed for RefSeq version
WGS Project:
CAJOSP01
Genome coverage:
76x
Linked assembly:
GCA_905333105.1 (alternate pseudohaplotype of diploid)

IDs: 9648991 [UID] 25816008 [GenBank] 30836098 [RefSeq]

See Genome Information for Maniola jurtina

Pathogen Detection Resources

There are 4 assemblies for this organism

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History (Show revision history)

Comment

The assembly ilManJurt1.1 is based on 76x PacBio data, 10X Genomics Chromium data, and Qiagen 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, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. The mitochondrial genome was assembled using MitoHifi. Finally, the 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 length402,038,846
Total ungapped length402,035,149
Gaps between scaffolds0
Number of scaffolds31
Scaffold N5015,090,120
Scaffold L5013
Number of contigs52
Contig N5013,288,869
Contig L5014
Total number of chromosomes and plasmids30
Number of component sequences (WGS or clone)31

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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_905333054.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1HG995207.1=NC_060029.10
Chromosome 2HG995209.1=NC_060030.10
Chromosome 3HG995210.1=NC_060031.10
Chromosome 4HG995211.1=NC_060032.10
Chromosome 5HG995212.1=NC_060033.10
Chromosome 6HG995213.1=NC_060034.10
Chromosome 7HG995214.1=NC_060035.10
Chromosome 8HG995215.1=NC_060036.10
Chromosome 9HG995216.1=NC_060037.10
Chromosome 10HG995217.1=NC_060038.10
Chromosome 11HG995218.1=NC_060039.10
Chromosome 12HG995219.1=NC_060040.10
Chromosome 13HG995220.1=NC_060041.10
Chromosome 14HG995221.1=NC_060042.10
Chromosome 15HG995222.1=NC_060043.10
Chromosome 16HG995223.1=NC_060044.10
Chromosome 17HG995224.1=NC_060045.10
Chromosome 18HG995225.1=NC_060046.10
Chromosome 19HG995226.1=NC_060047.10
Chromosome 20HG995227.1=NC_060048.10
Chromosome 21HG995228.1=NC_060049.10
Chromosome 22HG995229.1=NC_060050.10
Chromosome 23HG995230.1=NC_060051.10
Chromosome 24HG995231.1=NC_060052.10
Chromosome 25HG995232.1=NC_060053.10
Chromosome 26HG995233.1=NC_060054.10
Chromosome 27HG995235.1=NC_060055.10
Chromosome 28HG995236.1=NC_060056.10
Chromosome WHG995234.1=NC_060057.11
Chromosome ZHG995208.1=NC_060058.10

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule402,038,84631402,035,14915,090,120210
Chromosome 1Assembled molecule17,318,487117,318,47017,318,48710
Chromosome 2Assembled molecule17,186,260117,186,26017,186,26000
Chromosome 3Assembled molecule16,758,433116,757,73316,758,43320
Chromosome 4Assembled molecule16,671,097116,671,09716,671,09700
Chromosome 5Assembled molecule16,232,520116,232,52016,232,52000
Chromosome 6Assembled molecule16,201,745116,201,74516,201,74500
Chromosome 7Assembled molecule15,712,916115,712,81615,712,91610
Chromosome 8Assembled molecule15,421,669115,421,66915,421,66900
Chromosome 9Assembled molecule15,233,260115,233,06015,233,26010
Chromosome 10Assembled molecule15,174,349115,174,34915,174,34900
Chromosome 11Assembled molecule15,109,321115,109,27515,109,32110
Chromosome 12Assembled molecule15,090,120115,089,92015,090,12010
Chromosome 13Assembled molecule14,833,470114,833,47014,833,47000
Chromosome 14Assembled molecule14,702,743114,702,54314,702,74310
Chromosome 15Assembled molecule14,148,933114,148,93314,148,93300
Chromosome 16Assembled molecule14,033,434114,033,43414,033,43400
Chromosome 17Assembled molecule13,715,123113,714,92313,715,12310
Chromosome 18Assembled molecule13,539,626113,539,42613,539,62610
Chromosome 19Assembled molecule13,288,869113,288,86913,288,86900
Chromosome 20Assembled molecule13,275,689113,275,68913,275,68900
Chromosome 21Assembled molecule12,263,577112,262,94312,263,57750
Chromosome 22Assembled molecule12,131,722112,131,52212,131,72210
Chromosome 23Assembled molecule10,051,852110,051,85210,051,85200
Chromosome 24Assembled molecule9,430,11319,429,9139,430,11310
Chromosome 25Assembled molecule8,565,57118,565,3718,565,57110
Chromosome 26Assembled molecule7,754,45617,754,2567,754,45610
Chromosome 27Assembled molecule6,945,30216,945,3026,945,30200
Chromosome 28Assembled molecule6,657,72516,657,5256,657,72510
Chromosome WAllAssembled moleculeUnlocalized scaffolds7,384,4267,345,81138,6152117,384,2267,345,61138,6157,345,8117,345,81138,615110000
Chromosome ZAssembled molecule17,206,038117,206,03817,206,03800