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BPBGC_Ojam_1.0

Organism name:
Oxyura jamaicensis (ruddy duck)
Infraspecific name:
Breed: ruddy duck
Isolate:
SHBP4307
Sex:
female
BioSample:
SAMN13257492
BioProject:
PRJNA588796
Submitter:
Brood Parasitic Bird Genomes Consortium
Date:
2020/03/10
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_011077185.1 (latest)
RefSeq assembly accession:
GCF_011077185.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT
  • Data displayed for RefSeq version
WGS Project:
JAACYN01
Assembly method:
Supernova 2 v. SEPT-2019
Expected final version:
yes
Genome coverage:
60.0x
Sequencing technology:
Illumina NovaSeq

IDs: 6151271 [UID] 17483678 [GenBank] 20140218 [RefSeq]

See Genome Information for Oxyura jamaicensis

Pathogen Detection Resources

History (Show revision history)

Comment

Global statistics

Total sequence length1,147,585,764
Total ungapped length1,116,231,236
Gaps between scaffolds53
Number of scaffolds9,642
Scaffold N5036,145,614
Scaffold L509
Number of contigs28,026
Contig N50128,592
Contig L502,313
Total number of chromosomes and plasmids34
Number of component sequences (WGS or clone)28,026

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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_011077195.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM021799.1=NC_048893.1489
Chromosome 2CM021800.1=NC_048894.1352
Chromosome 3CM021801.1=NC_048895.1157
Chromosome 4CM021802.1=NC_048896.1120
Chromosome 5CM021803.1=NC_048897.191
Chromosome 6CM021804.1=NC_048898.158
Chromosome 7CM021805.1=NC_048899.146
Chromosome 8CM021806.1=NC_048900.165
Chromosome 9CM021807.1=NC_048901.144
Chromosome 10CM021808.1=NC_048902.127
Chromosome 11CM021809.1=NC_048903.137
Chromosome 12CM021810.1=NC_048904.134
Chromosome 13CM021811.1=NC_048905.129
Chromosome 14CM021812.1=NC_048906.160
Chromosome 15CM021813.1=NC_048907.138
Chromosome 16CM021814.1=NC_048908.115
Chromosome 17CM021815.1=NC_048909.137
Chromosome 18CM021816.1=NC_048910.130
Chromosome 19CM021817.1=NC_048911.137
Chromosome 20CM021818.1=NC_048912.118
Chromosome 21CM021819.1=NC_048913.119
Chromosome 22CM021820.1=NC_048914.143
Chromosome 23CM021821.1=NC_048915.143
Chromosome 24CM021822.1=NC_048916.18
Chromosome 25CM021823.1=NC_048917.145
Chromosome 26CM021824.1=NC_048918.137
Chromosome 27CM021825.1=NC_048919.174
Chromosome 28CM021826.1=NC_048920.161
Chromosome 30CM021827.1=NC_048921.132
Chromosome 31CM021828.1=NC_048922.128
Chromosome 32CM021829.1=NC_048923.120
Chromosome 33CM021830.1=NC_048924.1119
Chromosome WCM021832.1=NC_048925.172
Chromosome ZCM021831.1=NC_048926.1475
unplacedn/an/an/a6,695

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule1,147,585,7649,6421,116,231,23636,145,61418,38453
Chromosome 1AllAssembled moleculeUnlocalized scaffolds210,117,481204,625,1315,492,3504978489204,489,062199,014,7525,474,31071,492,74771,492,74723,8143,6633,58083770
Chromosome 2AllAssembled moleculeUnlocalized scaffolds161,169,342158,276,4972,892,8453553352157,536,350154,648,9952,887,35592,981,09492,981,09412,9462,6542,58272220
Chromosome 3AllAssembled moleculeUnlocalized scaffolds120,974,317118,540,9172,433,4001592157118,570,757116,320,7172,250,040116,102,589116,102,58931,3341,6691,62544110
Chromosome 4AllAssembled moleculeUnlocalized scaffolds98,199,35996,268,4921,930,867126612097,196,84995,267,7521,929,09751,682,00851,682,00857,1571,1761,15224550
Chromosome 5AllAssembled moleculeUnlocalized scaffolds66,221,69663,980,6472,241,0499329165,410,66663,171,6472,239,01954,585,72754,585,72763,91165664214110
Chromosome 6AllAssembled moleculeUnlocalized scaffolds38,073,89536,145,6141,928,2815915837,871,40835,958,5571,912,85136,145,61436,145,61472,8172942895000
Chromosome 7AllAssembled moleculeUnlocalized scaffolds40,216,83539,710,270506,5654934639,821,28539,314,720506,56533,669,26533,669,26528,3353643640220
Chromosome 8AllAssembled moleculeUnlocalized scaffolds32,377,93432,086,098291,8366616532,052,71431,761,718290,99632,086,09832,086,0986,02934132912000
Chromosome 9AllAssembled moleculeUnlocalized scaffolds27,003,69025,914,5501,089,1404514426,675,03025,606,1901,068,84025,914,55025,914,55058,3522552514000
Chromosome 10AllAssembled moleculeUnlocalized scaffolds22,556,88421,743,657813,2272812722,011,39421,411,217600,17721,743,65721,743,657114,52126123724000
Chromosome 11AllAssembled moleculeUnlocalized scaffolds22,232,11621,293,394938,7223923721,798,83621,062,224736,61211,238,01311,238,013497,85420418618110
Chromosome 12AllAssembled moleculeUnlocalized scaffolds22,248,74822,006,853241,8953513421,871,19821,630,913240,28522,006,85322,006,85311,71720919514000
Chromosome 13AllAssembled moleculeUnlocalized scaffolds20,715,20819,418,2751,296,9333122920,234,28819,062,8951,171,39312,002,70312,002,70397,40525223715110
Chromosome 14AllAssembled moleculeUnlocalized scaffolds17,863,48417,630,403233,0816116017,654,18417,421,743232,44117,630,40317,630,4036,02919718710000
Chromosome 15AllAssembled moleculeUnlocalized scaffolds15,314,06715,123,646190,4213913815,022,38714,832,906189,48115,123,64615,123,64610,99817316310000
Chromosome 16AllAssembled moleculeUnlocalized scaffolds769,444374,285395,15916115492,864258,135234,729267,670374,285267,670281612000
Chromosome 17AllAssembled moleculeUnlocalized scaffolds12,185,53311,762,718422,8153813711,916,37311,493,968422,40511,762,71811,762,71825,9861321275000
Chromosome 18AllAssembled moleculeUnlocalized scaffolds13,355,40412,583,665771,7393113012,803,46412,164,075639,38912,583,66512,583,665437,09416113823000
Chromosome 19AllAssembled moleculeUnlocalized scaffolds12,148,04711,651,985496,0623813711,991,55711,496,005495,55211,651,98511,651,98545,6501431385000
Chromosome 20AllAssembled moleculeUnlocalized scaffolds16,222,56715,907,983314,5842241816,094,12715,779,543314,58413,854,17813,854,17894,7151741740330
Chromosome 21AllAssembled moleculeUnlocalized scaffolds8,549,4568,430,007119,449212198,391,9668,272,847119,1194,986,1194,986,11910,5001141086110
Chromosome 22AllAssembled moleculeUnlocalized scaffolds5,773,2395,497,090276,149452435,343,9495,069,520274,4294,634,3054,634,30511,6841058916110
Chromosome 23AllAssembled moleculeUnlocalized scaffolds7,454,9157,097,135357,780441437,107,5756,801,145306,4307,097,1357,097,13513,13013111021000
Chromosome 24AllAssembled moleculeUnlocalized scaffolds7,708,4397,675,52432,9159187,637,7097,604,79432,9157,675,5247,675,5247,59277770000
Chromosome 25AllAssembled moleculeUnlocalized scaffolds2,950,6722,739,566211,106472452,412,5522,202,266210,2862,231,6732,231,6737,26212911910110
Chromosome 26AllAssembled moleculeUnlocalized scaffolds6,884,4286,727,800156,628381376,675,5686,519,950155,6186,727,8006,727,8007,03712411311000
Chromosome 27AllAssembled moleculeUnlocalized scaffolds6,509,1275,914,815594,312762745,818,7175,237,245581,4724,095,4794,095,47917,45714911831110
Chromosome 28AllAssembled moleculeUnlocalized scaffolds6,221,1485,735,600485,548621615,546,9195,104,541442,3785,735,6005,735,60014,07316412440000
Chromosome 30AllAssembled moleculeUnlocalized scaffolds657,503546,282111,22135332528,453418,592109,861195,317195,3175,268392019220
Chromosome 31AllAssembled moleculeUnlocalized scaffolds721,132530,036191,09629128487,742353,356134,386530,036530,036142,549422418000
Chromosome 32AllAssembled moleculeUnlocalized scaffolds95,62950,53845,0912442091,80947,22844,5816,36911,1532,3011046330
Chromosome 33AllAssembled moleculeUnlocalized scaffolds2,620,4162,245,791374,62512231192,168,0161,797,321370,695902,526902,5263,7601207842220
Chromosome WAllAssembled moleculeUnlocalized scaffolds1,018,146814,976203,17080872874,006671,496202,510213,742213,7423,401372512770
Chromosome ZAllAssembled moleculeUnlocalized scaffolds88,004,04982,654,0575,349,9924881347580,743,83875,938,4764,805,36210,180,22716,883,84415,3632,3662,23613012120
unplacedAssembled molecule32,451,4146,69530,887,6247,7451,7710