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bCapEur3.1

Organism name:
Caprimulgus europaeus (Eurasian nightjar)
BioSample:
SAMEA7524394
BioProject:
PRJEB44540
Submitter:
WELLCOME SANGER INSTITUTE
Date:
2021/05/17
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_907165065.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
CAJRAV01
Genome coverage:
87x
Linked assembly:
GCA_907165095.1 (alternate pseudohaplotype of diploid)

IDs: 10078971 [UID] 26794948 [GenBank]

See Genome Information for Caprimulgus europaeus

There are 2 assemblies for this organism

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History (Show revision history)

Comment

The assembly bCapEur3.1 is based on 87x PacBio data, 10X Genomics Chromium data, and Arima2 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 Falcon-unzip, retained haplotig separation with purge_dups, 10X based scaffolding with scaff10x, Arrow polishing assisted by Merfin, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with SALSA2. 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 length1,177,791,212
Total ungapped length1,177,765,377
Gaps between scaffolds0
Number of scaffolds121
Scaffold N5082,614,289
Scaffold L506
Number of contigs274
Contig N5030,622,946
Contig L5011
Total number of chromosomes and plasmids37
Number of component sequences (WGS or clone)121

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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 (GCA_907165064.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1OU015523.1n/an/a0
Chromosome 2OU015524.1n/an/a0
Chromosome 3OU015525.1n/an/a0
Chromosome 4OU015526.1n/an/a0
Chromosome 5OU015528.1n/an/a0
Chromosome 6OU015529.1n/an/a0
Chromosome 7OU015530.1n/an/a0
Chromosome 8OU015531.1n/an/a0
Chromosome 9OU015532.1n/an/a0
Chromosome 10OU015533.1n/an/a0
Chromosome 11OU015534.1n/an/a0
Chromosome 12OU015535.1n/an/a0
Chromosome 13OU015536.1n/an/a0
Chromosome 14OU015538.1n/an/a0
Chromosome 15OU015539.1n/an/a0
Chromosome 16OU015540.1n/an/a0
Chromosome 17OU015541.1n/an/a0
Chromosome 18OU015542.1n/an/a0
Chromosome 19OU015543.1n/an/a0
Chromosome 20OU015544.1n/an/a0
Chromosome 21OU015545.1n/an/a0
Chromosome 22OU015546.1n/an/a0
Chromosome 23OU015547.1n/an/a0
Chromosome 24OU015548.1n/an/a0
Chromosome 25OU015549.1n/an/a0
Chromosome 26OU015550.1n/an/a0
Chromosome 27OU015551.1n/an/a0
Chromosome 28OU015552.1n/an/a0
Chromosome 29OU015553.1n/an/a0
Chromosome 30OU015554.1n/an/a0
Chromosome 31OU015555.1n/an/a0
Chromosome 32OU015556.1n/an/a0
Chromosome 33OU015557.1n/an/a0
Chromosome 34OU015558.1n/an/a0
Chromosome 35OU015559.1n/an/a0
Chromosome WOU015537.1n/an/a0
Chromosome ZOU015527.1n/an/a0
unplacedn/an/an/a84

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All1,177,791,2121211,177,765,37782,614,2891530
Chromosome 1126,318,5101126,317,310126,318,51090
Chromosome 2125,369,5521125,368,052125,369,55290
Chromosome 3100,158,1361100,157,036100,158,13680
Chromosome 483,320,075183,319,27583,320,07560
Chromosome 582,614,289182,613,48982,614,28970
Chromosome 665,352,188165,351,58865,352,18840
Chromosome 760,467,248160,467,04860,467,24810
Chromosome 850,913,645150,913,34550,913,64530
Chromosome 948,660,147148,659,84748,660,14720
Chromosome 1043,004,850143,004,25043,004,85040
Chromosome 1135,230,674135,229,07435,230,67490
Chromosome 1223,520,972123,520,87223,520,97210
Chromosome 1322,807,378122,807,37822,807,37800
Chromosome 1422,349,459122,349,05922,349,45930
Chromosome 1519,400,540119,400,24019,400,54020
Chromosome 1618,743,433118,743,23318,743,43320
Chromosome 1716,934,410116,934,41016,934,41000
Chromosome 1815,699,869115,699,86915,699,86900
Chromosome 1913,782,655113,782,42013,782,65530
Chromosome 2012,518,677112,518,67712,518,67700
Chromosome 2112,349,417112,349,01712,349,41730
Chromosome 229,157,10019,156,7009,157,10040
Chromosome 238,187,40018,187,0008,187,40030
Chromosome 247,570,45917,570,3597,570,45910
Chromosome 257,538,74917,538,3497,538,74920
Chromosome 267,503,39917,503,3997,503,39900
Chromosome 276,260,69316,260,4936,260,69320
Chromosome 286,036,10616,035,7066,036,10640
Chromosome 293,387,42813,387,2283,387,42820
Chromosome 302,941,24712,940,5472,941,24750
Chromosome 312,473,18312,471,8832,473,18390
Chromosome 322,222,26912,221,3692,222,26940
Chromosome 331,263,71611,262,8161,263,71640
Chromosome 34563,3351563,235563,33510
Chromosome 35197,1181197,118197,11800
Chromosome W22,485,285122,483,43722,485,285100
Chromosome Z82,627,501182,626,20182,627,50190
unplaced7,860,100847,854,048236,727170
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