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Source database (GenBank or RefSeq) File type

SL3.0

This assembly has been replaced. See current version

Anomalous assembly.

Organism name:

Solanum lycopersicum (tomato)

Infraspecific name:

Cultivar: Heinz 1706

BioSample:

SAMN02981290

BioProject:

PRJNA119

Submitter:

Solanaceae Genomics Project

Date:

2018/04/18

Assembly level:

Chromosome

Genome representation:

full

Assembly anomaly:

contaminated

Excluded from RefSeq:

contaminated

GenBank assembly accession:

GCA_000188115.3 (replaced)

RefSeq assembly accession:

GCF_000188115.4 (replaced)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in RefSeq: chromosomes MT and Pltd

Data displayed for RefSeq version

WGS Project:

AEKE03

Assembly method:

Newbler v. v2.3; BioNano Irysview v. v2.3

Expected final version:

yes

Genome coverage:

27.0x

Sequencing technology:

454; Sanger; Illumina; SOLiD

IDs: 1681331 [UID] 6387548 [GenBank] 6973248 [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

In June 2022 84 sequences were suppressed because they were found to be contaminants.

Global statistics

Total sequence length	828,349,174
Total ungapped length	746,943,770
Gaps between scaffolds	0
Number of scaffolds	3,150
Scaffold N50	66,723,567
Scaffold L50	6
Number of contigs	22,704
Contig N50	133,207
Contig L50	1,333
Total number of chromosomes and plasmids	14
Number of component sequences (WGS or clone)	3,150

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	CM001064.3	=	NC_015438.3	0
Chromosome 2	CM001065.3	=	NC_015439.3	0
Chromosome 3	CM001066.3	=	NC_015440.3	0
Chromosome 4	CM001067.3	=	NC_015441.3	0
Chromosome 5	CM001068.3	=	NC_015442.3	0
Chromosome 6	CM001069.3	=	NC_015443.3	0
Chromosome 7	CM001070.3	=	NC_015444.3	0
Chromosome 8	CM001071.3	=	NC_015445.3	0
Chromosome 9	CM001072.3	=	NC_015446.3	0
Chromosome 10	CM001073.3	=	NC_015447.3	0
Chromosome 11	CM001074.3	=	NC_015448.3	0
Chromosome 12	CM001075.3	=	NC_015449.3	0
unplaced	n/a	n/a	n/a	3,136

Molecule name	GenBank ID		RefSeq ID
Mitochondrion MT	MF034192.1	=	NC_035963.1
Chloroplast Pltd	DQ347959.1	=	NC_007898.3

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps
All	827,747,456	3,148	746,342,052	66,723,567	19,554
Chromosome 1	98,455,869	1	88,005,260	98,455,869	1,409
Chromosome 2	55,977,580	1	48,705,832	55,977,580	1,166
Chromosome 3	72,290,146	1	61,528,713	72,290,146	1,849
Chromosome 4	66,557,038	1	60,616,392	66,557,038	1,857
Chromosome 5	66,723,567	1	61,604,619	66,723,567	1,971
Chromosome 6	49,794,276	1	43,960,411	49,794,276	1,163
Chromosome 7	68,175,699	1	62,453,334	68,175,699	1,651
Chromosome 8	65,987,440	1	60,271,492	65,987,440	1,426
Chromosome 9	72,906,345	1	65,413,034	72,906,345	1,575
Chromosome 10	65,633,393	1	63,114,748	65,633,393	904
Chromosome 11	56,597,135	1	50,740,846	56,597,135	1,532
Chromosome 12	68,126,176	1	62,126,574	68,126,176	1,763
unplaced	20,522,792	3,136	17,800,797	17,797	1,288

Molecule	Total Length
All	601,718
Mitochondrion MT	446,257
Chloroplast Pltd	155,461

Assembly

Genome Assembly

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SL3.0

See Genome Information for Solanum lycopersicum

Pathogen Detection Resources

There are 32 assemblies for this organism

History (Show revision history)

Comment

Global statistics

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Assembly Unit Name
Primary Assembly
non-nuclear