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Source database (GenBank or RefSeq) File type

C.cajan_V1.0

This assembly has been replaced. See current version

Anomalous assembly.

Organism name:

Cajanus cajan (pigeon pea)

BioSample:

SAMN02981370

BioProject:

PRJNA72815

Submitter:

BGI

Date:

2016/09/29

Assembly level:

Chromosome

Genome representation:

full

Assembly anomaly:

contaminated

Excluded from RefSeq:

contaminated

GenBank assembly accession:

GCA_000340665.1 (replaced)

RefSeq assembly accession:

GCF_000340665.1 (replaced)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in RefSeq: chromosome Pltd

Data displayed for RefSeq version

WGS Project:

AGCT01

Assembly method:

SOAPdenovo v. 1.05

Genome coverage:

160x

Sequencing technology:

Illumina Hiseq2000

IDs: 711901 [UID] 3149988 [GenBank] 4160098 [RefSeq]

See Genome Information for Cajanus cajan

Pathogen Detection Resources

There are 3 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_000340665.2	≠	GCF_000340665.2	C.cajan_V1.1	Chromosome	Latest GenBank, Latest RefSeq
GCA_000340665.1	≠	GCF_000340665.1	C.cajan_V1.0	Chromosome	Replaced GenBank, Replaced RefSeq

Comment

Annotated scaffolds were added in March 2016.
In May 2022 5089 sequences were suppressed because they were found to be contaminants.

Global statistics

Total sequence length	592,970,700
Total ungapped length	558,535,405
Gaps between scaffolds	0
Number of scaffolds	36,536
Scaffold N50	555,764
Scaffold L50	72
Number of contigs	72,923
Contig N50	22,480
Contig L50	7,524
Total number of chromosomes and plasmids	12
Number of component sequences (WGS or clone)	72,923

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	CM003603.1	=	NC_033804.1	0
Chromosome 2	CM003604.1	=	NC_033805.1	0
Chromosome 3	CM003605.1	=	NC_033806.1	0
Chromosome 4	CM003606.1	=	NC_033807.1	0
Chromosome 5	CM003607.1	=	NC_033808.1	0
Chromosome 6	CM003608.1	=	NC_033809.1	0
Chromosome 7	CM003609.1	=	NC_033810.1	0
Chromosome 8	CM003610.1	=	NC_033811.1	0
Chromosome 9	CM003611.1	=	NC_033812.1	0
Chromosome 10	CM003612.1	=	NC_033813.1	0
Chromosome 11	CM003613.1	=	NC_033814.1	0
unplaced	n/a	n/a	n/a	36,524

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps
All	592,816,859	36,535	558,381,564	555,764	36,387
Chromosome 1	17,676,265	1	16,811,428	17,676,265	1,106
Chromosome 2	36,921,656	1	35,209,314	36,921,656	2,396
Chromosome 3	29,476,785	1	28,270,687	29,476,785	1,824
Chromosome 4	12,502,730	1	11,881,937	12,502,730	829
Chromosome 5	5,133,333	1	4,917,493	5,133,333	335
Chromosome 6	23,791,330	1	22,726,967	23,791,330	1,519
Chromosome 7	19,579,009	1	18,663,605	19,579,009	1,219
Chromosome 8	20,383,548	1	19,495,582	20,383,548	1,216
Chromosome 9	10,489,139	1	10,060,195	10,489,139	590
Chromosome 10	22,571,102	1	21,405,194	22,571,102	1,438
Chromosome 11	48,970,052	1	46,448,885	48,970,052	3,181
unplaced	345,321,910	36,524	322,490,277	181,687	20,734

Assembly

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C.cajan_V1.0

See Genome Information for Cajanus cajan

Pathogen Detection Resources

There are 3 assemblies for this organism

History (Show revision history)

Comment

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Assembly Unit Name
Primary Assembly
non-nuclear