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KH

Organism name:
Ciona intestinalis (vase tunicate)
BioProject:
PRJDA65419
Submitter:
Organization: Department of Zoology, Graduate School of
Date:
2011/04/29
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_000224145.1 (replaced)
RefSeq assembly accession:
GCF_000224145.1 (replaced)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Different: chromosome MT.
  • A partial mitochondrial genome contig in the GenBank assembly was replaced by a complete mitochondrial genome sequence in the RefSeq assembly.
  • Data displayed for RefSeq version
WGS Project:
EAAA01

IDs: 527578 [UID] 300498 [GenBank] 527578 [RefSeq]

See Genome Information for Ciona intestinalis

There are 2 assemblies for this organism

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History (Show revision history)

Comment

This less-fragmented assembly (called as the KH assmebly) was generated from the version 1 assembly by an evidence-based process of scaffold joining, coupled with the removal of small scaffolds that did not appear to contain expressed genes or that ... appeared to be variant duplicates of regions better represented in other scaffolds.
The largest scaffolds representing each of Ciona's 14 chromosomes are named KHCx, where x is the chromosome number.
See detailed assembly procedure and nomenclature in the reference. The KH assembly can be browsed in the Ghost Database. URL: http://ghost.zool.kyoto-u.ac.jp/indexr1.html
This submitted assembly sequence is slightly different from the original KH assembly. Short (<20nt) sequences intervened between two gap sequences (or between a gap and a scaffold end) are replaced with stretches of 'N's. The original KH assembly is available in the above web site.  more

Global statistics

Total sequence length115,227,500
Total assembly gap length3,063,510
Gaps between scaffolds0
Number of scaffolds1,272
Scaffold N505,152,901
Scaffold L509
Number of contigs6,381
Contig N5037,096
Contig L50875
Total number of chromosomes and plasmids15
Number of component sequences (WGS or clone)6,374

Supplemental Content

PubMed articles for this assembly

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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_000224155.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1HT000001.1=NC_020166.10
Chromosome 2HT000007.1=NC_020167.10
Chromosome 3HT000008.1=NC_020168.10
Chromosome 4HT000009.1=NC_020169.10
Chromosome 5HT000010.1=NC_020170.10
Chromosome 6HT000011.1=NC_020171.10
Chromosome 7HT000012.1=NC_020172.10
Chromosome 8HT000013.1=NC_020173.10
Chromosome 9HT000014.1=NC_020174.10
Chromosome 10HT000002.1=NC_020175.10
Chromosome 11HT000003.1=NC_020176.10
Chromosome 12HT000004.1=NC_020177.10
Chromosome 13HT000005.1=NC_020178.10
Chromosome 14HT000006.1=NC_020179.10
unplacedn/an/an/a1,257

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All115,212,7101,271112,149,2005,152,9015,1250
Chromosome 110,041,00519,692,51210,041,0054250
Chromosome 27,758,92517,478,6577,758,9252830
Chromosome 36,703,98916,496,7446,703,9892330
Chromosome 45,505,74815,375,4615,505,7482030
Chromosome 55,035,97014,979,5115,035,9701980
Chromosome 62,365,71112,332,1812,365,711740
Chromosome 76,125,20916,005,3976,125,2092520
Chromosome 86,398,79516,256,2046,398,7952260
Chromosome 96,586,23716,504,0386,586,2372290
Chromosome 104,880,87514,788,7244,880,8752150
Chromosome 115,152,90115,046,9555,152,9012010
Chromosome 125,356,12415,192,8955,356,1242210
Chromosome 131,792,67911,721,1731,792,679720
Chromosome 144,591,98714,476,7454,591,9871920
unplaced36,916,5551,25735,802,00398,0702,1010
MoleculeTotal
Length
Mitochondrion MT14,790
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