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Source database (GenBank or RefSeq) File type

bStrHab1.2.pri

Organism name:

Strigops habroptila (Kakapo)

Isolate:

Jane

Sex:

female

BioSample:

SAMN09948751

BioProject:

PRJNA489135

Submitter:

Vertebrate Genomes Project

Date:

2020/03/04

Assembly level:

Chromosome

Genome representation:

full

RefSeq category:

representative genome

GenBank assembly accession:

GCA_004027225.2 (latest)

RefSeq assembly accession:

GCF_004027225.2 (latest)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in GenBank: chromosome MT (in non-nuclear assembly-unit)

Data displayed for RefSeq version

WGS Project:

RXXE02

Assembly method:

FALCON v. 5.1.1; FALCON unzip v. 1.0.2; scaff10X v. git 4.28.2018; Bionano Solve DLS v. 3.2.1; Salsa2 HiC v. 2.0; smrtanalysis Arrow polishing & gap filling v. 5.1.0.26412; longranger align v. 2.2.2; freebayes v. 1.2.0; purge_haplotigs v. bit 7.10.2018; gEVAL manual curation v. 2019-11-08

Expected final version:

Genome coverage:

76.1x

Sequencing technology:

PacBio RSII; 10X Genomics linked reads; Bionano Genomics DLS; Arima Genomics HiC

IDs: 6098431 [UID] 17349718 [GenBank] 17492068 [RefSeq]

See Genome Information for Strigops habroptila

Pathogen Detection Resources

There are 2 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_004027225.2	≠	GCF_004027225.2	bStrHab1.2.pri	Chromosome	Latest GenBank, Latest RefSeq
GCA_004027225.1	≠	GCF_004027225.1	bStrHab1_v1.p	Chromosome	Replaced GenBank, Replaced RefSeq

Comment

The chromosome names were updated in August 2019 when the sex chromosomes were identified. Former chromosome 3 is chromosome Z, former chromosome 13 is chromosome W, and the remaining former chromosomes 3-26 were renamed sequentially to chromosomes 4-24 (4-12 ... are now 3-11, and 14-26 are now 12-24, respectively).

This is an updated assembly of GCA_004027225.1. New Hi-C mapping tools (HiGlass) and experience of the VGP with bird genomes were used to re-curate the assembly (using gEVAL), where nearly all previously unlocalized scaffolds are now assembled into their respective chromosomes

This assembly represents the principal haplotype of the diploid genome Strigops habroptila and includes the chromosomes. The alternate haplotype sequences are in WGS project RXXF00000000.  more

Global statistics

Total sequence length	1,148,597,545
Total ungapped length	1,138,053,485
Gaps between scaffolds	0
Number of scaffolds	89
Scaffold N50	83,240,647
Scaffold L50	6
Number of contigs	456
Contig N50	9,454,087
Contig L50	40
Total number of chromosomes and plasmids	25
Number of component sequences (WGS or clone)	89

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	CM013761.2	=	NC_044277.2	0
Chromosome 2	CM013762.2	=	NC_044278.2	0
Chromosome 3	CM013764.2	=	NC_044279.2	0
Chromosome 4	CM013765.1	=	NC_046358.1	0
Chromosome 5	CM013766.2	=	NC_044281.2	0
Chromosome 6	CM013767.2	=	NC_044282.2	0
Chromosome 7	CM013768.2	=	NC_044283.2	0
Chromosome 8	CM013769.2	=	NC_044284.2	0
Chromosome 9	CM013770.2	=	NC_044285.2	0
Chromosome 10	CM013771.1	=	NC_046359.1	0
Chromosome 11	CM013772.1	=	NC_046360.1	0
Chromosome 12	CM013774.2	=	NC_044288.2	0
Chromosome 13	CM013775.2	=	NC_044289.2	1
Chromosome 14	CM013776.2	=	NC_044290.2	0
Chromosome 15	CM013777.2	=	NC_044291.2	0
Chromosome 16	CM013778.2	=	NC_044292.2	0
Chromosome 17	CM013779.2	=	NC_044293.2	0
Chromosome 18	CM013780.2	=	NC_044294.2	0
Chromosome 19	CM013781.2	=	NC_044295.2	0
Chromosome 20	CM013782.2	=	NC_044296.2	0
Chromosome 21	CM013783.2	=	NC_044297.2	0
Chromosome 22	CM013784.2	=	NC_044298.2	0
Chromosome 23	CM013785.2	=	NC_044299.2	0
Chromosome W	CM013773.2	=	NC_044301.2	0
Chromosome Z	CM013763.2	=	NC_044302.2	0
unplaced	n/a	n/a	n/a	63

Molecule	Sequence Role	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps	Unspanned Gaps
All	Assembled molecule	1,148,597,545	89	1,138,053,485	83,240,647	367	0
Chromosome 1	Assembled molecule	155,644,563	1	155,274,428	155,644,563	27	0
Chromosome 2	Assembled molecule	123,023,803	1	122,681,959	123,023,803	13	0
Chromosome 3	Assembled molecule	89,082,643	1	88,893,043	89,082,643	11	0
Chromosome 4	Assembled molecule	86,460,390	1	86,234,915	86,460,390	17	0
Chromosome 5	Assembled molecule	83,240,647	1	83,167,368	83,240,647	12	0
Chromosome 6	Assembled molecule	76,431,904	1	74,967,335	76,431,904	12	0
Chromosome 7	Assembled molecule	70,131,234	1	70,100,132	70,131,234	9	0
Chromosome 8	Assembled molecule	63,488,934	1	63,420,797	63,488,934	9	0
Chromosome 9	Assembled molecule	44,431,488	1	44,325,567	44,431,488	10	0
Chromosome 10	Assembled molecule	43,764,472	1	43,737,777	43,764,472	6	0
Chromosome 11	Assembled molecule	39,187,110	1	38,287,087	39,187,110	5	0
Chromosome 12	Assembled molecule	27,433,492	1	27,379,456	27,433,492	4	0
Chromosome 13	AllAssembled moleculeUnlocalized scaffolds	28,700,55816,476,16012,224,398	211	28,424,98216,322,52012,102,462	16,476,16016,476,16012,224,398	1156	000
Chromosome 14	Assembled molecule	12,884,122	1	12,884,109	12,884,122	1	0
Chromosome 15	Assembled molecule	12,307,978	1	12,144,597	12,307,978	4	0
Chromosome 16	Assembled molecule	8,419,051	1	8,419,051	8,419,051	0	0
Chromosome 17	Assembled molecule	7,441,144	1	7,005,045	7,441,144	4	0
Chromosome 18	Assembled molecule	6,734,548	1	6,734,548	6,734,548	0	0
Chromosome 19	Assembled molecule	5,789,228	1	5,789,228	5,789,228	0	0
Chromosome 20	Assembled molecule	5,645,757	1	5,354,023	5,645,757	7	0
Chromosome 21	Assembled molecule	5,492,648	1	5,457,787	5,492,648	2	0
Chromosome 22	Assembled molecule	2,907,026	1	2,707,983	2,907,026	6	0
Chromosome 23	Assembled molecule	2,785,283	1	2,507,490	2,785,283	7	0
Chromosome W	Assembled molecule	37,425,726	1	33,718,034	37,425,726	112	0
Chromosome Z	Assembled molecule	101,869,369	1	101,016,501	101,869,369	38	0
unplaced	Assembled molecule	7,874,427	63	7,420,243	253,776	40	0

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bStrHab1.2.pri

See Genome Information for Strigops habroptila

Pathogen Detection Resources

There are 2 assemblies for this organism

History (Show revision history)

Comment

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