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Source database (GenBank or RefSeq) File type

mPhoSin1.pri

Organism name:

Phocoena sinus (vaquita)

Isolate:

mPhoSin1

Sex:

female

BioSample:

SAMN12325353

BioProject:

PRJNA557831

Submitter:

Vertebrate Genomes Project

Date:

2019/09/26

Assembly type:

haploid (principal pseudohaplotype of diploid)

Assembly level:

Chromosome

Genome representation:

full

RefSeq category:

representative genome

GenBank assembly accession:

GCA_008692025.1 (latest)

RefSeq assembly accession:

GCF_008692025.1 (latest)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in GenBank: chromosome MT

Data displayed for RefSeq version

WGS Project:

VOSU01

Assembly method:

FALCON v. 5.1.1; FALCON-Unzip v. 1.0.2; Arrow smrtanalysis Pacbio polishing v. 6.0.0.47841; purge_haplotigs v. 1.0.4; scaff10X v. 4.1; Bionano solve DLS v. 3.3_10252018; Salsa HiC v. 2.2; Arrow smrtanalysis Pacbio polishing & gap filling v. 6.0.0.47841; longranger align v. 2.2.2; freebayes Illumina polishing v. 1.2.0; gEVAL manual curation v. 2019-07-23; VGP assembly pipeline individual v. 1.5

Expected final version:

Genome coverage:

67.26x

Sequencing technology:

PacBio Sequel I; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLE-1

Linked assembly:

GCA_008692045.1 (alternate pseudohaplotype of diploid)

IDs: 4726381 [UID] 14079358 [GenBank] 16682018 [RefSeq]

See Genome Information for Phocoena sinus

Pathogen Detection Resources

There are 2 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_008692025.1	≠	GCF_008692025.1	mPhoSin1.pri	Chromosome	Latest GenBank, Latest RefSeq

Comment

This assembly represents the principal haplotype of the diploid genome Phocoena sinus and includes the chromosomes. The alternate haplotype sequences are in WGS project VOSV00000000.

Global statistics

Total sequence length	2,371,524,154
Total ungapped length	2,363,478,510
Gaps between scaffolds	0
Number of scaffolds	64
Scaffold N50	115,469,292
Scaffold L50	8
Number of contigs	272
Contig N50	20,218,762
Contig L50	39
Total number of chromosomes and plasmids	22
Number of component sequences (WGS or clone)	64

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	CM018156.1	=	NC_045763.1	0
Chromosome 2	CM018157.1	=	NC_045764.1	0
Chromosome 3	CM018158.1	=	NC_045765.1	0
Chromosome 4	CM018159.1	=	NC_045766.1	0
Chromosome 5	CM018160.1	=	NC_045767.1	0
Chromosome 6	CM018161.1	=	NC_045768.1	0
Chromosome 7	CM018162.1	=	NC_045769.1	0
Chromosome 8	CM018163.1	=	NC_045770.1	0
Chromosome 9	CM018164.1	=	NC_045771.1	0
Chromosome 10	CM018165.1	=	NC_045772.1	0
Chromosome 11	CM018166.1	=	NC_045773.1	0
Chromosome 12	CM018167.1	=	NC_045774.1	0
Chromosome 13	CM018168.1	=	NC_045775.1	0
Chromosome 14	CM018169.1	=	NC_045776.1	0
Chromosome 15	CM018170.1	=	NC_045777.1	0
Chromosome 16	CM018171.1	=	NC_045778.1	0
Chromosome 17	CM018172.1	=	NC_045779.1	0
Chromosome 18	CM018173.1	=	NC_045780.1	0
Chromosome 19	CM018174.1	=	NC_045781.1	0
Chromosome 20	CM018175.1	=	NC_045782.1	0
Chromosome 21	CM018176.1	=	NC_045783.1	0
Chromosome X	CM018177.1	=	NC_045784.1	0
unplaced	n/a	n/a	n/a	42

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps
All	2,371,524,154	64	2,363,478,510	115,469,292	208
Chromosome 1	185,845,356	1	185,038,194	185,845,356	14
Chromosome 2	178,563,925	1	177,701,665	178,563,925	11
Chromosome 3	174,291,665	1	173,357,052	174,291,665	17
Chromosome 4	146,127,150	1	145,806,927	146,127,150	12
Chromosome 5	139,762,554	1	139,761,932	139,762,554	8
Chromosome 6	115,952,311	1	115,761,213	115,952,311	10
Chromosome 7	115,469,292	1	115,440,414	115,469,292	5
Chromosome 8	110,408,561	1	110,087,163	110,408,561	13
Chromosome 9	106,736,052	1	106,601,222	106,736,052	6
Chromosome 10	102,828,027	1	102,656,227	102,828,027	6
Chromosome 11	104,118,372	1	103,743,558	104,118,372	5
Chromosome 12	90,399,378	1	90,246,299	90,399,378	6
Chromosome 13	90,400,161	1	90,145,531	90,400,161	7
Chromosome 14	89,762,611	1	89,518,322	89,762,611	4
Chromosome 15	88,287,594	1	87,516,967	88,287,594	9
Chromosome 16	85,252,673	1	84,689,567	85,252,673	10
Chromosome 17	79,603,858	1	79,602,457	79,603,858	7
Chromosome 18	79,885,847	1	79,846,664	79,885,847	3
Chromosome 19	59,501,331	1	59,222,164	59,501,331	4
Chromosome 20	58,878,645	1	58,878,361	58,878,645	5
Chromosome 21	35,802,323	1	35,767,759	35,802,323	3
Chromosome X	131,664,873	1	130,114,851	131,664,873	35
unplaced	1,981,595	42	1,974,001	78,647	8

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mPhoSin1.pri

See Genome Information for Phocoena sinus

Pathogen Detection Resources

There are 2 assemblies for this organism

History (Show revision history)

Comment

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