fPseGeo1.1

This assembly has been replaced. See current version

Organism name:: Pseudochaenichthys georgianus (South Georgia icefish)
BioSample:: SAMEA104132832
BioProject:: PRJEB37648
Submitter:: SC
Date:: 2020/04/15
Assembly type:: haploid (principal pseudohaplotype of diploid)
Assembly level:: Chromosome
Genome representation:: full
RefSeq category:: representative genome
GenBank assembly accession:: GCA_902827115.1 (replaced)
RefSeq assembly accession:: GCF_902827115.1 (latest)
RefSeq assembly and GenBank assembly identical:: yes
WGS Project:: CADEHP01
Genome coverage:: 93x

IDs: 6932051 [UID] 19129508 [GenBank] 19360538 [RefSeq]

See Genome Information for Pseudochaenichthys georgianus

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_902827115.2	n/a	n/a	fPseGeo1.2	Chromosome	Latest GenBank
GCA_902827115.1	=	GCF_902827115.1	fPseGeo1.1	Chromosome	Latest RefSeq, Replaced GenBank

Comment

The assembly fPseGeo1.1 is based on 93x PacBio data, 56x 10X Genomics Chromium data, and 41x Dovetail Hi-C data generated at the Wellcome Sanger Institute. The assembly process included the following sequence of steps: initial PacBio assembly generation with ... Falcon-unzip, retained haplotig identification with Purge Haplotigs, 10X based scaffolding with scaff10x, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL, and further retained haplotigs were identified using purge_dups. Chromosome-scale scaffolds are named by synteny to medaka.  more

Global statistics

Total sequence length	1,026,101,545
Total ungapped length	1,025,462,058
Gaps between scaffolds	0
Number of scaffolds	1,563
Scaffold N50	42,832,159
Scaffold L50	11
Number of contigs	4,021
Contig N50	661,283
Contig L50	431
Total number of chromosomes and plasmids	24
Number of component sequences (WGS or clone)	1,563

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	LR792546.1	=	NC_047503.1	0
Chromosome 2	LR792547.1	=	NC_047504.1	0
Chromosome 3	LR792548.1	=	NC_047505.1	0
Chromosome 4	LR792549.1	=	NC_047506.1	0
Chromosome 5	LR792550.1	=	NC_047507.1	0
Chromosome 6	LR792551.1	=	NC_047508.1	0
Chromosome 7	LR792552.1	=	NC_047509.1	0
Chromosome 8	LR792553.1	=	NC_047510.1	0
Chromosome 9	LR792554.1	=	NC_047511.1	0
Chromosome 10	LR792555.1	=	NC_047512.1	0
Chromosome 11	LR792556.1	=	NC_047513.1	0
Chromosome 12	LR792557.1	=	NC_047514.1	0
Chromosome 13	LR792558.1	=	NC_047515.1	0
Chromosome 14	LR792559.1	=	NC_047516.1	0
Chromosome 15	LR792560.1	=	NC_047517.1	0
Chromosome 16	LR792561.1	=	NC_047518.1	0
Chromosome 17	LR792562.1	=	NC_047519.1	0
Chromosome 18	LR792563.1	=	NC_047520.1	0
Chromosome 19	LR792564.1	=	NC_047521.1	0
Chromosome 20	LR792565.1	=	NC_047522.1	0
Chromosome 21	LR792566.1	=	NC_047523.1	0
Chromosome 22	LR792567.1	=	NC_047524.1	0
Chromosome 23	LR792568.1	=	NC_047525.1	0
Chromosome 24	LR792569.1	=	NC_047526.1	0
unplaced	n/a	n/a	n/a	1,539

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps
All	1,026,101,545	1,563	1,025,462,058	42,832,159	2,458
Chromosome 1	49,975,704	1	49,952,725	49,975,704	113
Chromosome 2	12,615,095	1	12,589,336	12,615,095	45
Chromosome 3	53,425,585	1	53,398,649	53,425,585	134
Chromosome 4	46,382,498	1	46,355,835	46,382,498	114
Chromosome 5	46,241,663	1	46,218,600	46,241,663	103
Chromosome 6	45,575,153	1	45,551,148	45,575,153	116
Chromosome 7	45,376,657	1	45,356,520	45,376,657	93
Chromosome 8	35,372,779	1	35,351,643	35,372,779	88
Chromosome 9	48,837,966	1	48,813,016	48,837,966	103
Chromosome 10	46,365,164	1	46,333,290	46,365,164	111
Chromosome 11	33,597,571	1	33,581,481	33,597,571	76
Chromosome 12	30,946,200	1	30,934,839	30,946,200	51
Chromosome 13	42,832,159	1	42,806,248	42,832,159	102
Chromosome 14	40,811,654	1	40,788,686	40,811,654	96
Chromosome 15	39,528,010	1	39,507,495	39,528,010	82
Chromosome 16	47,693,014	1	47,665,469	47,693,014	121
Chromosome 17	43,034,850	1	43,015,838	43,034,850	99
Chromosome 18	24,387,387	1	24,368,619	24,387,387	72
Chromosome 19	28,991,432	1	28,968,647	28,991,432	86
Chromosome 20	24,389,971	1	24,375,750	24,389,971	63
Chromosome 21	39,591,329	1	39,576,322	39,591,329	68
Chromosome 22	35,435,734	1	35,420,076	35,435,734	79
Chromosome 23	25,555,492	1	25,541,819	25,555,492	61
Chromosome 24	35,305,502	1	35,288,279	35,305,502	77
unplaced	103,832,976	1,539	103,701,728	110,672	305

Assembly

Genome Assembly

Result Filters

Organism group

Status

Assembly level

RefSeq category

Exclude

Annotation status

Taxonomy check status

Relation to type material

Assembly type

Sequence release date

Custom date range

Contig N50

Custom range

Scaffold N50

Custom range

Additional filters

Send to:

Download Assembly

fPseGeo1.1

See Genome Information for Pseudochaenichthys georgianus

Pathogen Detection Resources

There are 2 assemblies for this organism

History (Show revision history)

Comment

Global statistics

Supplemental Content

Access the data

Assembly Information

Related Information

Recent activity

Global assembly definition

Assembly statistics