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Source database (GenBank or RefSeq) File type

ASM3116895v1

Organism name:

Gadus macrocephalus (Pacific cod)

Isolate:

Gmac_GOA_2020

BioSample:

SAMN33716189

BioProject:

PRJNA943286

Submitter:

NOAA Fisheries

Date:

2023/09/05

Assembly level:

Chromosome

Genome representation:

full

RefSeq category:

representative genome

GenBank assembly accession:

GCA_031168955.1 (latest)

RefSeq assembly accession:

GCF_031168955.1 (latest)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in RefSeq: chromosome MT

Data displayed for RefSeq version

Assembly method:

We used PacBio HiFi in HiFiasm (version 0.16.1-r375) for assembly and phasing. This was followed by Proximo scaffolding (this is internal software that does not have a formal version) and finished using Juicebox (version 1.11.08). v. see text

Expected final version:

yes

Reference guided assembly:

Gadmor3.0

Genome coverage:

45x

Sequencing technology:

PacBio

IDs: 18381581 [UID] 46980398 [GenBank] 47594378 [RefSeq]

See Genome Information for Gadus macrocephalus

Pathogen Detection Resources

There are 3 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_031168955.1	≠	GCF_031168955.1	ASM3116895v1	Chromosome	Latest GenBank, Latest RefSeq

Comment

Genome-Annotation-Data

##Genome-Annotation-Data-START##Annotation Provider::NCBI RefSeq
Annotation Status::Full annotation
Annotation Name::GCF_031168955.1-RS_2023_09
Annotation Pipeline::NCBI eukaryotic genome annotation pipeline
Annotation Software Version::10.2
URL Organism::Gadus_macrocephalus
Annotation Method::Gnomon; cmsearch; tRNAscan-SE
Features Annotated::Gene; mRNA; CDS; ncRNA
##Genome-Annotation-Data-END##

Global statistics

Total sequence length	555,697,652
Total ungapped length	555,215,489
Gaps between scaffolds	0
Number of scaffolds	24
Scaffold N50	24,646,214
Scaffold L50	10
Number of contigs	4,850
Contig N50	202,622
Contig L50	606
Total number of chromosomes and plasmids	24
Number of component sequences (WGS or clone)	24

Molecule name	GenBank sequence		RefSeq sequence
Chromosome 1	CP133525.1	=	NC_082382.1
Chromosome 2	CP133526.1	=	NC_082383.1
Chromosome 3	CP133527.1	=	NC_082384.1
Chromosome 4	CP133528.1	=	NC_082385.1
Chromosome 5	CP133529.1	=	NC_082386.1
Chromosome 6	CP133530.1	=	NC_082387.1
Chromosome 7	CP133531.1	=	NC_082388.1
Chromosome 8	CP133532.1	=	NC_082389.1
Chromosome 9	CP133533.1	=	NC_082390.1
Chromosome 10	CP133534.1	=	NC_082391.1
Chromosome 11	CP133535.1	=	NC_082392.1
Chromosome 12	CP133536.1	=	NC_082393.1
Chromosome 13	CP133537.1	=	NC_082394.1
Chromosome 14	CP133538.1	=	NC_082395.1
Chromosome 15	CP133539.1	=	NC_082396.1
Chromosome 16	CP133540.1	=	NC_082397.1
Chromosome 17	CP133541.1	=	NC_082398.1
Chromosome 18	CP133542.1	=	NC_082399.1
Chromosome 19	CP133543.1	=	NC_082400.1
Chromosome 20	CP133544.1	=	NC_082401.1
Chromosome 21	CP133545.1	=	NC_082402.1
Chromosome 22	CP133546.1	=	NC_082403.1
Chromosome 23	CP133547.1	=	NC_082404.1

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps
All	555,681,083	23	555,198,920	24,646,214	4,826
Chromosome 1	26,289,739	1	26,264,996	26,289,739	248
Chromosome 2	23,805,147	1	23,783,863	23,805,147	213
Chromosome 3	26,984,552	1	26,961,552	26,984,552	230
Chromosome 4	35,077,496	1	35,049,496	35,077,496	280
Chromosome 5	22,175,970	1	22,157,370	22,175,970	186
Chromosome 6	27,900,680	1	27,877,852	27,900,680	229
Chromosome 7	28,186,669	1	28,160,430	28,186,669	263
Chromosome 8	23,760,065	1	23,739,165	23,760,065	209
Chromosome 9	23,393,856	1	23,375,474	23,393,856	184
Chromosome 10	23,728,004	1	23,706,604	23,728,004	214
Chromosome 11	26,267,057	1	26,245,613	26,267,057	215
Chromosome 12	27,587,113	1	27,566,283	27,587,113	208
Chromosome 13	22,312,454	1	22,290,854	22,312,454	216
Chromosome 14	26,048,790	1	26,027,406	26,048,790	214
Chromosome 15	24,646,214	1	24,627,714	24,646,214	185
Chromosome 16	29,952,890	1	29,932,590	29,952,890	203
Chromosome 17	16,295,523	1	16,278,323	16,295,523	172
Chromosome 18	21,077,965	1	21,059,222	21,077,965	188
Chromosome 19	17,993,618	1	17,976,132	17,993,618	176
Chromosome 20	23,303,860	1	23,286,060	23,303,860	178
Chromosome 21	19,478,734	1	19,458,834	19,478,734	199
Chromosome 22	19,411,328	1	19,389,928	19,411,328	214
Chromosome 23	20,003,359	1	19,983,159	20,003,359	202

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ASM3116895v1

See Genome Information for Gadus macrocephalus

Pathogen Detection Resources

There are 3 assemblies for this organism

History (Show revision history)

Comment

Genome-Annotation-Data

Global statistics

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Assembly Unit Name
Primary Assembly
non-nuclear