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Source database (GenBank or RefSeq) File type

SL2.50

This assembly has been replaced. See current version

Description:

Solyc2.50

Organism name:

Solanum lycopersicum (tomato)

Infraspecific name:

Cultivar: Heinz 1706

BioSample:

SAMN02981290

BioProject:

PRJNA119

Submitter:

Solanaceae Genomics Project

Date:

2014/10/16

Assembly level:

Chromosome

Genome representation:

full

GenBank assembly accession:

GCA_000188115.2 (replaced)

RefSeq assembly accession:

GCF_000188115.3 (replaced)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in RefSeq: chromosome Pltd

Data displayed for RefSeq version

WGS Project:

AEKE02

Assembly method:

Newbler v. 2.3-PostRelease-01/11/2010

Genome coverage:

27x

Sequencing technology:

454; Sanger; Illumina; SOLiD

IDs: 217231 [UID] 1362528 [GenBank] 1382708 [RefSeq]

See Genome Information for Solanum lycopersicum

Pathogen Detection Resources

There are 32 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_000188115.4	≠	GCF_000188115.5	SL3.1	Chromosome	Latest GenBank, Latest RefSeq
GCA_000188115.3	≠	GCF_000188115.4	SL3.0	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_000188115.2	≠	GCF_000188115.3	SL2.50	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_000188115.1	≠	GCF_000188115.2	SL2.40	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_000188115.1	≠	GCF_000188115.1	SL2.40	Chromosome	Replaced GenBank, Replaced RefSeq

Comment

This is the combined tomato genome assembly, made from whole-genome shotgun and full BAC sequences. The approximate coverage is: 454 reads (filtered, 22X), BAC end Sanger reads (0.18X), Fosmid end Sanger reads (0.087X), selected BAC mixture (SBM) Sanger reads ... (5.2X).
In assembly SL2.50, released in October 2014, the tomato genome scaffolds from build SL2.40 were re-ordered and re-oriented, and the gap sizes between scaffolds were set using FISH and optical mapping.  more

Global statistics

Total sequence length	823,786,402
Total ungapped length	737,791,897
Gaps between scaffolds	79
Number of scaffolds	3,224
Scaffold N50	16,467,796
Scaffold L50	17
Number of contigs	26,880
Contig N50	86,952
Contig L50	2,009
Total number of chromosomes and plasmids	13
Number of component sequences (WGS or clone)	26,878

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	CM001064.2	=	NC_015438.2	0
Chromosome 2	CM001065.2	=	NC_015439.2	0
Chromosome 3	CM001066.2	=	NC_015440.2	0
Chromosome 4	CM001067.2	=	NC_015441.2	0
Chromosome 5	CM001068.2	=	NC_015442.2	0
Chromosome 6	CM001069.2	=	NC_015443.2	0
Chromosome 7	CM001070.2	=	NC_015444.2	0
Chromosome 8	CM001071.2	=	NC_015445.2	0
Chromosome 9	CM001072.2	=	NC_015446.2	0
Chromosome 10	CM001073.2	=	NC_015447.2	0
Chromosome 11	CM001074.2	=	NC_015448.2	0
Chromosome 12	CM001075.2	=	NC_015449.2	0
unplaced	n/a	n/a	n/a	3,132

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps	Unspanned Gaps
All	823,630,941	3,223	737,636,436	16,467,796	23,656	79
Chromosome 1	98,543,444	9	86,120,078	20,460,048	2,423	8
Chromosome 2	55,340,444	7	47,257,016	11,730,995	1,392	6
Chromosome 3	70,787,664	13	60,861,821	6,990,560	2,109	12
Chromosome 4	66,470,942	6	60,449,024	17,595,704	1,925	5
Chromosome 5	65,875,088	3	61,240,635	42,121,211	2,112	2
Chromosome 6	49,751,636	8	43,572,957	8,601,227	1,319	7
Chromosome 7	68,045,021	4	61,960,815	33,282,180	1,860	3
Chromosome 8	65,866,657	9	59,784,694	8,418,108	1,615	8
Chromosome 9	72,482,091	10	64,867,797	19,241,881	1,737	9
Chromosome 10	65,527,505	6	60,791,186	16,467,796	2,180	5
Chromosome 11	56,302,525	6	50,257,288	15,176,445	1,741	5
Chromosome 12	67,145,203	10	61,806,392	16,091,949	1,900	9
unplaced	21,492,721	3,132	18,666,733	27,516	1,343	0

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SL2.50

See Genome Information for Solanum lycopersicum

Pathogen Detection Resources

There are 32 assemblies for this organism

History (Show revision history)

Comment

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Assembly Unit Name
Primary Assembly
non-nuclear