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LupAngTanjil_v1.0

Organism name:
Lupinus angustifolius (narrow-leaved blue lupine)
Infraspecific name:
Cultivar: Tanjil
BioSample:
SAMN04215042
BioProject:
PRJNA299755
Submitter:
CSIRO
Date:
2016/11/16
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_001865875.1 (latest)
RefSeq assembly accession:
GCF_001865875.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
MLAU01
Assembly method:
CutAdapt v. 1.1; FLASH v. 1.2.2; Kmerfreq v. 2015-05-28; SOAPdenovo2 v. 2015-05-28; SSPACE2 v. 2.0; BGI GapCloser v. 2015-05-28
Expected final version:
no
Genome coverage:
245.0x
Sequencing technology:
Illumina HiSeq 2500

IDs: 890181 [UID] 3727208 [GenBank] 3768438 [RefSeq]

See Genome Information for Lupinus angustifolius

There are 3 assemblies for this organism

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History (Show revision history)

Comment

Sequencing was done with Illumina HiSeq 2500 paired-ends and Illumina HiSeq 2500 mate-paired. This assembly was constructed with CutAdapt (min length 25 bp, rounds 3, match length 5 bp) v. 1.1; FLASH (mate-paired 3' overlap read pairs discarded) v. ... 1.2.2; Kmerfreq v. 2015-05-28; SOAPdenovo2 (PE only) v. 2015-05-28; SSPACE2 (5 rounds per library insert size, ascending size order) v. 2.0; BGI GapCloser (5 rounds, PE libraries only) v. 2015-05-28 and 100kb BAC-end scaffolding - Bambus (range 50-400,000) v. 2015-05-28. Gaps of unknown size >10 bp were converted to 100bp, Repeatmasker(-no _is -norna -noint) and Tandem Repeats Finder (2 7 7 80 10 50 50 -f -d -m -h) were run, and then sequences were discarded if they were < 200 bp length OR >= 50% repetitive, simple repeat or unknown N bases. LG mapping was done via ePCR (<=2gap, <=2mis, amplicon 10-1000bp(Fluidigm) 10-5000bp(other)) and Glycine max synteny: MUMmer (promer --mum --filter, >=90% sim).  more

Global statistics

Total sequence length609,203,021
Total ungapped length605,049,621
Gaps between scaffolds805
Number of scaffolds14,378
Scaffold N50702,610
Scaffold L50232
Number of contigs55,107
Contig N5048,365
Contig L503,139
Total number of chromosomes and plasmids20
Number of component sequences (WGS or clone)55,107

Supplemental Content

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_001865885.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome LG01CM007361.1=NC_032009.10
Chromosome LG02CM007362.1=NC_032010.10
Chromosome LG03CM007363.1=NC_032011.10
Chromosome LG04CM007364.1=NC_032012.10
Chromosome LG05CM007365.1=NC_032013.10
Chromosome LG06CM007366.1=NC_032014.10
Chromosome LG07CM007367.1=NC_032015.10
Chromosome LG08CM007368.1=NC_032016.10
Chromosome LG09CM007369.1=NC_032017.10
Chromosome LG10CM007370.1=NC_032018.10
Chromosome LG11CM007371.1=NC_032019.10
Chromosome LG12CM007372.1=NC_032020.10
Chromosome LG13CM007373.1=NC_032021.10
Chromosome LG14CM007374.1=NC_032022.10
Chromosome LG15CM007375.1=NC_032023.10
Chromosome LG16CM007376.1=NC_032024.10
Chromosome LG17CM007377.1=NC_032025.10
Chromosome LG18CM007378.1=NC_032026.10
Chromosome LG19CM007379.1=NC_032027.10
Chromosome LG20CM007380.1=NC_032028.10
unplacedn/an/an/a13,553

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All609,203,02114,378605,049,621702,61040,729805
Chromosome LG0136,457,5815136,205,4811,362,8252,47150
Chromosome LG0224,697,6525124,529,452702,6101,63250
Chromosome LG0330,153,0195629,888,319960,2012,59255
Chromosome LG0427,333,9754227,149,4751,081,5511,80441
Chromosome LG0526,376,9115126,178,511871,3721,93450
Chromosome LG0633,111,4505232,893,3501,058,5412,13051
Chromosome LG0719,782,1703519,666,570771,6221,12234
Chromosome LG0825,521,6464025,357,646972,7991,60139
Chromosome LG0921,753,7124821,578,412815,8601,70647
Chromosome LG1016,341,9553116,235,255736,6521,03730
Chromosome LG1135,963,9586535,670,058769,9022,87564
Chromosome LG1219,065,7013118,935,801877,9251,26930
Chromosome LG1317,820,6803217,704,680877,7201,12931
Chromosome LG1416,251,7772516,134,377993,0281,15024
Chromosome LG1520,964,7034320,814,803891,6091,45742
Chromosome LG1620,786,8813020,635,0811,255,9701,48929
Chromosome LG1721,299,8803121,142,1801,174,1951,54730
Chromosome LG1816,588,0073516,481,107804,8781,03534
Chromosome LG1918,159,8123618,019,212737,1941,37135
Chromosome LG2021,988,5904021,852,490949,5511,32239
unplaced138,782,96113,553137,977,36145,3668,0560
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