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ilVanCard2.1

Organism name:
Vanessa cardui (painted lady)
BioSample:
SAMEA7523147
BioProject:
PRJEB42869
Submitter:
WELLCOME SANGER INSTITUTE
Date:
2021/02/16
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_905220365.1 (replaced)
RefSeq assembly accession:
GCF_905220365.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT
  • Data displayed for RefSeq version
WGS Project:
CAJMZP01
Genome coverage:
25x
Linked assembly:
GCA_905220355.1 (alternate pseudohaplotype of diploid)

IDs: 9308331 [UID] 25060668 [GenBank] 32220588 [RefSeq]

See Genome Information for Vanessa cardui

Pathogen Detection Resources

There are 3 assemblies for this organism

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History (Show revision history)

Comment

The assembly ilVanCard2.1 is based on 25x PacBio data, 10X Genomics Chromium data, and Arima 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 length424,798,336
Total ungapped length424,772,036
Gaps between scaffolds0
Number of scaffolds36
Scaffold N5014,615,999
Scaffold L5014
Number of contigs127
Contig N507,041,724
Contig L5023
Total number of chromosomes and plasmids32
Number of component sequences (WGS or clone)36

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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_905220364.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1LR999925.1=NC_061123.10
Chromosome 2LR999926.1=NC_061124.10
Chromosome 3LR999927.1=NC_061125.10
Chromosome 4LR999928.1=NC_061126.10
Chromosome 5LR999929.1=NC_061127.10
Chromosome 6LR999930.1=NC_061128.10
Chromosome 7LR999931.1=NC_061129.10
Chromosome 8LR999932.1=NC_061130.10
Chromosome 9LR999933.1=NC_061131.10
Chromosome 10LR999934.1=NC_061132.10
Chromosome 11LR999935.1=NC_061133.10
Chromosome 12LR999936.1=NC_061134.10
Chromosome 13LR999937.1=NC_061135.10
Chromosome 14LR999938.1=NC_061136.10
Chromosome 15LR999939.1=NC_061137.10
Chromosome 16LR999941.1=NC_061138.10
Chromosome 17LR999942.1=NC_061139.10
Chromosome 18LR999943.1=NC_061140.10
Chromosome 19LR999944.1=NC_061141.10
Chromosome 20LR999945.1=NC_061142.10
Chromosome 21LR999946.1=NC_061143.10
Chromosome 22LR999947.1=NC_061144.10
Chromosome 23LR999948.1=NC_061145.10
Chromosome 24LR999949.1=NC_061146.10
Chromosome 25LR999950.1=NC_061147.10
Chromosome 26LR999951.1=NC_061148.10
Chromosome 27LR999952.1=NC_061149.10
Chromosome 28LR999953.1=NC_061150.10
Chromosome 29LR999954.1=NC_061151.10
Chromosome 30LR999955.1=NC_061152.10
Chromosome WLR999940.1=NC_061153.14
Chromosome ZLR999924.1=NC_061154.10

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule424,798,33636424,772,03614,615,999910
Chromosome 1Assembled molecule16,607,008116,606,30816,607,00820
Chromosome 2Assembled molecule16,362,069116,361,36916,362,06920
Chromosome 3Assembled molecule16,090,551116,089,95116,090,55130
Chromosome 4Assembled molecule16,000,791116,000,39116,000,79120
Chromosome 5Assembled molecule15,952,094115,951,39415,952,09420
Chromosome 6Assembled molecule15,715,213115,714,71315,715,21310
Chromosome 7Assembled molecule15,572,524115,571,92415,572,52430
Chromosome 8Assembled molecule15,426,761115,425,36115,426,76140
Chromosome 9Assembled molecule15,296,561115,295,76115,296,56140
Chromosome 10Assembled molecule14,945,938114,945,23814,945,93820
Chromosome 11Assembled molecule14,868,897114,867,69714,868,89730
Chromosome 12Assembled molecule14,774,369114,773,46914,774,36930
Chromosome 13Assembled molecule14,615,999114,615,49914,615,99910
Chromosome 14Assembled molecule14,605,406114,604,30614,605,40640
Chromosome 15Assembled molecule13,916,383113,916,18313,916,38310
Chromosome 16Assembled molecule13,774,036113,773,83613,774,03610
Chromosome 17Assembled molecule13,550,656113,550,15613,550,65610
Chromosome 18Assembled molecule13,236,624113,235,52413,236,62440
Chromosome 19Assembled molecule12,933,853112,933,25312,933,85330
Chromosome 20Assembled molecule12,861,081112,860,58112,861,08110
Chromosome 21Assembled molecule12,594,674112,594,07412,594,67430
Chromosome 22Assembled molecule11,704,087111,703,38711,704,08720
Chromosome 23Assembled molecule11,326,783111,326,38311,326,78320
Chromosome 24Assembled molecule11,199,261111,198,76111,199,26110
Chromosome 25Assembled molecule9,960,13719,960,1379,960,13700
Chromosome 26Assembled molecule9,839,93419,838,9349,839,93420
Chromosome 27Assembled molecule8,262,36918,261,5698,262,36940
Chromosome 28Assembled molecule8,178,46818,177,8688,178,46830
Chromosome 29Assembled molecule7,379,29717,378,4977,379,29740
Chromosome 30Assembled molecule6,166,33416,165,4346,166,33430
Chromosome WAllAssembled moleculeUnlocalized scaffolds14,039,88213,819,298220,58451414,034,18213,814,098220,08413,819,29813,819,29848,36018171000
Chromosome ZAssembled molecule17,040,296117,039,89617,040,29620