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Source database (GenBank or RefSeq) File type

fSpaAur1.1

This assembly has been replaced. See current version

Organism name:

Sparus aurata (gilthead seabream)

BioSample:

SAMEA104384835

BioProject:

PRJEB31901

Submitter:

Date:

2019/07/30

Assembly type:

haploid (principal pseudohaplotype of diploid)

Assembly level:

Chromosome

Genome representation:

full

RefSeq category:

representative genome

GenBank assembly accession:

GCA_900880675.1 (replaced)

RefSeq assembly accession:

GCF_900880675.1 (latest)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in RefSeq: chromosome MT

Data displayed for RefSeq version

WGS Project:

CAAHFC01

Genome coverage:

56x

Linked assembly:

GCA_900880695.1 (alternate pseudohaplotype of diploid)

IDs: 4213601 [UID] 12898238 [GenBank] 12983138 [RefSeq]

See Genome Information for Sparus aurata

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_900880675.2	n/a	n/a	fSpaAur1.2	Chromosome	Latest GenBank
GCA_900880675.1	≠	GCF_900880675.1	fSpaAur1.1	Chromosome	Latest RefSeq, Replaced GenBank

Comment

The assembly fSpaAur1.1 is based on 
56x PacBio Sequel data, 
62x coverage Illumina HiSeqX data from a 10X Genomics Chromium library generated at the Wellcome Sanger Institute, as well as 
71x coverage HiSeqX data from a Hi-C library prepared ... by Arima Genomics. An initial PacBio assembly was made using Falcon-unzip, and retained haplotigs were identified using purge_haplotigs. The primary contigs were then scaffolded using the 10X data with scaff10x, then scaffolded further using the Hi-C data with SALSA2. Polishing and gap-filling of both the primary scaffolds and haplotigs was performed using the PacBio reads and Arrow, followed by two rounds of Illumina polishing using the 10X data and freebayes. Finally, the assembly was manually improved using gEVAL to correct mis-joins and improve concordance with the raw data. Chromosomes are named according to synteny with the GCA_003309015.1 assembly of Sparus aurata.  more

Global statistics

Total sequence length	833,595,063
Total ungapped length	833,252,801
Gaps between scaffolds	0
Number of scaffolds	176
Scaffold N50	35,791,275
Scaffold L50	11
Number of contigs	1,224
Contig N50	2,862,625
Contig L50	75
Total number of chromosomes and plasmids	25
Number of component sequences (WGS or clone)	176

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	LR537121.1	=	NC_044187.1	0
Chromosome 2	LR537122.1	=	NC_044188.1	0
Chromosome 3	LR537123.1	=	NC_044189.1	0
Chromosome 4	LR537124.1	=	NC_044190.1	0
Chromosome 5	LR537125.1	=	NC_044191.1	0
Chromosome 6	LR537126.1	=	NC_044192.1	0
Chromosome 7	LR537127.1	=	NC_044193.1	0
Chromosome 8	LR537128.1	=	NC_044194.1	0
Chromosome 9	LR537129.1	=	NC_044195.1	0
Chromosome 10	LR537130.1	=	NC_044196.1	0
Chromosome 11	LR537131.1	=	NC_044197.1	0
Chromosome 12	LR537132.1	=	NC_044198.1	0
Chromosome 13	LR537133.1	=	NC_044199.1	0
Chromosome 14	LR537134.1	=	NC_044200.1	0
Chromosome 15	LR537135.1	=	NC_044201.1	0
Chromosome 16	LR537136.1	=	NC_044202.1	0
Chromosome 17	LR537137.1	=	NC_044203.1	0
Chromosome 18	LR537138.1	=	NC_044204.1	0
Chromosome 19	LR537139.1	=	NC_044205.1	0
Chromosome 20	LR537140.1	=	NC_044206.1	0
Chromosome 21	LR537141.1	=	NC_044207.1	0
Chromosome 22	LR537142.1	=	NC_044208.1	0
Chromosome 23	LR537143.1	=	NC_044209.1	0
Chromosome 24	LR537144.1	=	NC_044210.1	0
unplaced	n/a	n/a	n/a	151

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps
All	833,578,411	175	833,236,149	35,791,275	1,048
Chromosome 1	41,035,582	1	41,022,379	41,035,582	51
Chromosome 2	36,133,474	1	36,120,503	36,133,474	48
Chromosome 3	32,888,385	1	32,876,712	32,888,385	41
Chromosome 4	41,392,777	1	41,373,796	41,392,777	57
Chromosome 5	38,249,111	1	38,230,362	38,249,111	45
Chromosome 6	40,124,345	1	40,104,545	40,124,345	54
Chromosome 7	35,997,798	1	35,981,613	35,997,798	55
Chromosome 8	36,959,192	1	36,947,546	36,959,192	33
Chromosome 9	37,012,328	1	36,996,428	37,012,328	40
Chromosome 10	35,512,760	1	35,491,698	35,512,760	65
Chromosome 11	35,380,617	1	35,365,647	35,380,617	45
Chromosome 12	30,193,437	1	30,183,447	30,193,437	31
Chromosome 13	35,791,275	1	35,772,026	35,791,275	67
Chromosome 14	25,861,820	1	25,848,828	25,861,820	37
Chromosome 15	31,859,785	1	31,849,663	31,859,785	29
Chromosome 16	30,078,578	1	30,064,414	30,078,578	43
Chromosome 17	37,948,182	1	37,938,813	37,948,182	33
Chromosome 18	37,104,330	1	37,099,131	37,104,330	23
Chromosome 19	31,047,742	1	31,032,545	31,047,742	45
Chromosome 20	28,386,240	1	28,378,667	28,386,240	29
Chromosome 21	35,160,130	1	35,146,030	35,160,130	43
Chromosome 22	31,425,404	1	31,417,320	31,425,404	25
Chromosome 23	30,526,999	1	30,519,099	30,526,999	23
Chromosome 24	22,435,136	1	22,423,036	22,435,136	38
unplaced	15,072,984	151	15,051,901	160,859	48

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fSpaAur1.1

See Genome Information for Sparus aurata

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