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SL2.50

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 (in non-nuclear assembly-unit)
  • 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

There are 8 assemblies for this organism

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History (Show revision history)

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 length823,786,402
Total ungapped length737,791,897
Gaps between scaffolds79
Number of scaffolds3,224
Scaffold N5016,467,796
Scaffold L5017
Number of contigs26,880
Contig N5086,952
Contig L502,009
Total number of chromosomes and plasmids13
Number of component sequences (WGS or clone)26,878

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
non-nuclear
Assembly Unit: Primary Assembly (GCF_000188125.2)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM001064.2=NC_015438.20
Chromosome 2CM001065.2=NC_015439.20
Chromosome 3CM001066.2=NC_015440.20
Chromosome 4CM001067.2=NC_015441.20
Chromosome 5CM001068.2=NC_015442.20
Chromosome 6CM001069.2=NC_015443.20
Chromosome 7CM001070.2=NC_015444.20
Chromosome 8CM001071.2=NC_015445.20
Chromosome 9CM001072.2=NC_015446.20
Chromosome 10CM001073.2=NC_015447.20
Chromosome 11CM001074.2=NC_015448.20
Chromosome 12CM001075.2=NC_015449.20
unplacedn/an/an/a3,132

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All823,630,9413,223737,636,43616,467,79623,65679
Chromosome 198,543,444986,120,07820,460,0482,4238
Chromosome 255,340,444747,257,01611,730,9951,3926
Chromosome 370,787,6641360,861,8216,990,5602,10912
Chromosome 466,470,942660,449,02417,595,7041,9255
Chromosome 565,875,088361,240,63542,121,2112,1122
Chromosome 649,751,636843,572,9578,601,2271,3197
Chromosome 768,045,021461,960,81533,282,1801,8603
Chromosome 865,866,657959,784,6948,418,1081,6158
Chromosome 972,482,0911064,867,79719,241,8811,7379
Chromosome 1065,527,505660,791,18616,467,7962,1805
Chromosome 1156,302,525650,257,28815,176,4451,7415
Chromosome 1267,145,2031061,806,39216,091,9491,9009
unplaced21,492,7213,13218,666,73327,5161,3430
MoleculeTotal
Length
Chloroplast Pltd155,461
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