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Source database (GenBank or RefSeq) File type

fPerMag1.pri

This assembly has been replaced. See current version

Organism name:

Periophthalmus magnuspinnatus (bony fishes)

Isolate:

fPerMag1

Sex:

female

BioSample:

SAMN12629500

BioProject:

PRJNA561998

Submitter:

Vertebrate Genomes Project

Date:

2020/01/03

Assembly type:

haploid (principal pseudohaplotype of diploid)

Assembly level:

Chromosome

Genome representation:

full

GenBank assembly accession:

GCA_009829125.1 (replaced)

RefSeq assembly accession:

GCF_009829125.1 (replaced)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Different: chromosome MT.

Data displayed for RefSeq version

WGS Project:

WNMA01

Assembly method:

FALCON v. 2018.31.08-03.06; FALCON-Unzip v. 6.0.0.47841; purge_dups v. 51544-08-31; scaff10x v. 4.1.0; Bionano Solve DLS v. 3.2.1; Salsa HiC v. 2.2; Arrow smrtanalysis Pacbio polishing & gap filling v. 6.0.0.47841; longranger align v. 2.2.2; freebayes Illumina polishing v. 1.3.1; gEVAL manual curation v. 2019-10-11; VGP assembly pipeline individual v. 1.6

Expected final version:

Genome coverage:

69.53x

Sequencing technology:

PacBio Sequel I CLR; llumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS

Linked assembly:

GCA_009829135.1 (alternate pseudohaplotype of diploid)

IDs: 5432801 [UID] 15730408 [GenBank] 19124248 [RefSeq]

See Genome Information for Periophthalmus magnuspinnatus

Pathogen Detection Resources

There are 4 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_009829125.3	≠	GCF_009829125.3	fPerMag1.2.pri	Chromosome	Latest GenBank, Latest RefSeq
GCA_009829125.2	≠	GCF_009829125.2	fPerMag1.pri_v2	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_009829125.1	≠	GCF_009829125.1	fPerMag1.pri	Chromosome	Replaced GenBank, Replaced RefSeq

Comment

This assembly represents the principal haplotype of the diploid genome Periophthalmus magnuspinnatus and includes the chromosomes. The alternate haplotype sequences are in WGS project WNMB00000000

This genome was updated in March 2023. Improved Hi-C mapping shows that this assembly has ... only 24 chromosomes. Chromosome 25 and its associated contig (CM020615, WNMA01000025) were removed from the assembly. This sequence was found to be a part of chromosome 11, so the chromosome 11 sequence and its associated contig sequence (CM020601, WNMA01000013) were also updated.  more

Global statistics

Total sequence length	752,621,858
Total ungapped length	745,443,304
Gaps between scaffolds	0
Number of scaffolds	124
Scaffold N50	32,865,169
Scaffold L50	11
Number of contigs	822
Contig N50	2,301,275
Contig L50	87
Total number of chromosomes and plasmids	26
Number of component sequences (WGS or clone)	124

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	CM020591.1	=	NC_047126.1	0
Chromosome 2	CM020592.1	=	NC_047127.1	0
Chromosome 3	CM020593.1	=	NC_047128.1	0
Chromosome 4	CM020594.1	=	NC_047129.1	0
Chromosome 5	CM020595.1	=	NC_047130.1	0
Chromosome 6	CM020596.1	=	NC_047131.1	0
Chromosome 7	CM020597.1	=	NC_047132.1	0
Chromosome 8	CM020598.1	=	NC_047133.1	0
Chromosome 9	CM020599.1	=	NC_047134.1	0
Chromosome 10	CM020600.1	=	NC_047135.1	0
Chromosome 11	CM020601.1	=	NC_047136.1	0
Chromosome 12	CM020602.1	=	NC_047137.1	0
Chromosome 13	CM020603.1	=	NC_047138.1	0
Chromosome 14	CM020604.1	=	NC_047139.1	0
Chromosome 15	CM020605.1	=	NC_047140.1	0
Chromosome 16	CM020606.1	=	NC_047141.1	0
Chromosome 17	CM020607.1	=	NC_047142.1	0
Chromosome 18	CM020608.1	=	NC_047143.1	0
Chromosome 19	CM020609.1	=	NC_047144.1	0
Chromosome 20	CM020610.1	=	NC_047145.1	0
Chromosome 21	CM020611.1	=	NC_047146.1	0
Chromosome 22	CM020612.1	=	NC_047147.1	0
Chromosome 23	CM020613.1	=	NC_047148.1	0
Chromosome 24	CM020614.1	=	NC_047149.1	0
Chromosome 25	CM020615.1	=	NC_047150.1	0
unplaced	n/a	n/a	n/a	98

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps
All	752,605,361	123	745,426,807	32,865,169	698
Chromosome 1	36,052,970	1	35,500,690	36,052,970	36
Chromosome 2	19,540,339	1	19,539,026	19,540,339	9
Chromosome 3	36,957,123	1	36,605,467	36,957,123	30
Chromosome 4	35,021,165	1	34,954,713	35,021,165	34
Chromosome 5	34,011,676	1	33,993,441	34,011,676	37
Chromosome 6	33,835,733	1	33,588,739	33,835,733	29
Chromosome 7	34,908,682	1	34,782,087	34,908,682	40
Chromosome 8	29,687,151	1	29,685,725	29,687,151	13
Chromosome 9	36,171,850	1	36,073,768	36,171,850	35
Chromosome 10	36,988,977	1	36,640,712	36,988,977	32
Chromosome 11	30,435,919	1	30,399,688	30,435,919	26
Chromosome 12	19,532,153	1	19,421,258	19,532,153	15
Chromosome 13	32,620,125	1	32,047,058	32,620,125	46
Chromosome 14	32,379,725	1	31,645,032	32,379,725	18
Chromosome 15	32,865,169	1	32,583,326	32,865,169	26
Chromosome 16	33,977,497	1	33,751,885	33,977,497	36
Chromosome 17	31,521,007	1	31,339,934	31,521,007	31
Chromosome 18	28,378,236	1	27,818,634	28,378,236	35
Chromosome 19	29,583,991	1	27,762,280	29,583,991	26
Chromosome 20	28,068,090	1	27,671,483	28,068,090	23
Chromosome 21	33,436,419	1	33,295,368	33,436,419	35
Chromosome 22	29,018,424	1	28,867,648	29,018,424	20
Chromosome 23	24,170,445	1	24,029,657	24,170,445	15
Chromosome 24	27,914,776	1	27,909,437	27,914,776	31
Chromosome 25	2,028,439	1	2,027,432	2,028,439	5
unplaced	3,499,280	98	3,492,319	52,581	15

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fPerMag1.pri

See Genome Information for Periophthalmus magnuspinnatus

Pathogen Detection Resources

There are 4 assemblies for this organism

History (Show revision history)

Comment

Global statistics

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Assembly Unit Name
Primary Assembly
non-nuclear