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Source database (GenBank or RefSeq) File type

Cucumber_9930_V3

Organism name:

Cucumis sativus (cucumber)

Infraspecific name:

Cultivar: 9930

BioSample:

SAMN02953750

BioProject:

PRJNA33619

Submitter:

The Cucumber Genome Initiative

Date:

2019/11/15

Assembly level:

Chromosome

Genome representation:

full

RefSeq category:

representative genome

GenBank assembly accession:

GCA_000004075.3 (latest)

RefSeq assembly accession:

GCF_000004075.3 (latest)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in RefSeq: chromosomes 1, 2, 3, Pltd

Data displayed for RefSeq version

WGS Project:

ACHR03

Assembly method:

Celera Assembler v. 1.8; FALCON v. 0.3

Expected final version:

Genome coverage:

50.0x

Sequencing technology:

PacBio RSII; PacBio Sequel; 10X Genomics; Hi-C; Illumina

IDs: 5324161 [UID] 15412838 [GenBank] 15585248 [RefSeq]

See Genome Information for Cucumis sativus

Pathogen Detection Resources

There are 14 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_000004075.3	≠	GCF_000004075.3	Cucumber_9930_V3	Chromosome	Latest GenBank, Latest RefSeq
GCA_000004075.2	≠	GCF_000004075.2	ASM407v2	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_000004075.1	≠	GCF_000004075.1	CucSat_1.0	Scaffold	Replaced GenBank, Replaced RefSeq

Comment

Gaps of 10bp were created by 10X Genomics, and gaps of 500bp were created by Hi-C technology

Global statistics

Total sequence length	226,640,966
Total ungapped length	226,604,796
Gaps between scaffolds	0
Number of scaffolds	88
Scaffold N50	31,125,843
Scaffold L50	4
Number of contigs	177
Contig N50	8,937,712
Contig L50	9
Total number of chromosomes and plasmids	11
Number of component sequences (WGS or clone)	88

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	CM002922.2	=	NC_026655.2	0
Chromosome 2	CM002923.2	=	NC_026656.2	0
Chromosome 3	CM002924.2	=	NC_026657.2	0
Chromosome 4	CM002925.2	=	NC_026658.2	0
Chromosome 5	CM002926.2	=	NC_026659.2	0
Chromosome 6	CM002927.2	=	NC_026660.2	0
Chromosome 7	CM002928.2	=	NC_026661.2	0
unplaced	n/a	n/a	n/a	77

Molecule name	GenBank ID		RefSeq ID
Mitochondrion 1	HQ860792.1	=	NC_016005.1
Mitochondrion 2	HQ860794.1	=	NC_016004.1
Mitochondrion 3	HQ860793.1	=	NC_016006.1
Chloroplast Pltd	AJ970307.1	=	NC_007144.1

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps
All	224,801,081	84	224,764,911	31,125,843	89
Chromosome 1	32,926,272	1	32,920,242	32,926,272	15
Chromosome 2	24,837,039	1	24,833,009	24,837,039	11
Chromosome 3	40,877,379	1	40,875,369	40,877,379	5
Chromosome 4	26,827,763	1	26,821,223	26,827,763	17
Chromosome 5	31,913,682	1	31,909,652	31,913,682	11
Chromosome 6	31,125,843	1	31,118,343	31,125,843	15
Chromosome 7	22,466,726	1	22,460,726	22,466,726	12
unplaced	13,826,377	77	13,826,347	181,498	3

Molecule	Total Length
All	1,839,885
Mitochondrion 1	1,555,935
Mitochondrion 2	83,817
Mitochondrion 3	44,840
Chloroplast Pltd	155,293

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Cucumber_9930_V3

See Genome Information for Cucumis sativus

Pathogen Detection Resources

There are 14 assemblies for this organism

History (Show revision history)

Comment

Global statistics

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Assembly Unit Name
Primary Assembly
non-nuclear