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Source database (GenBank or RefSeq) File type

aMicUni1.1

This assembly has been replaced. See current version

Organism name:

Microcaecilia unicolor (caecilians)

BioSample:

SAMEA104387962

BioProject:

PRJEB32737

Submitter:

Date:

2019/06/22

Assembly type:

haploid (principal pseudohaplotype of diploid)

Assembly level:

Chromosome

Genome representation:

full

RefSeq category:

representative genome

GenBank assembly accession:

GCA_901765095.1 (replaced)

RefSeq assembly accession:

GCF_901765095.1 (latest)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in RefSeq: chromosome MT

Data displayed for RefSeq version

WGS Project:

CABFKK01

Genome coverage:

53x

Linked assembly:

GCA_901765105.1 (alternate pseudohaplotype of diploid)

IDs: 3813451 [UID] 12058288 [GenBank] 12716908 [RefSeq]

See Genome Information for Microcaecilia unicolor

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_901765095.2	n/a	n/a	aMicUni1.2	Chromosome	Latest GenBank
GCA_901765095.1	≠	GCF_901765095.1	aMicUni1.1	Chromosome	Latest RefSeq, Replaced GenBank

Comment

The assembly aMicUni1.1 is based on 
53x PacBio data, 
52x coverage 10X Genomics Chromium data, BioNano data and 
25x coverage Arima Hi-C data generated at the Wellcome Sanger Institute. The assembly process included the following sequence of steps: initial ... PacBio assembly generation with Falcon-unzip, retained haplotig identification with Purge Haplotigs, 10X based scaffolding with scaff10x, BioNano hybrid-scaffolding, Hi-C based scaffolding with SALSA2, Arrow polishing, and two rounds of FreeBayes polishing. Finally, the assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size.  more

Global statistics

Total sequence length	4,685,939,420
Total ungapped length	4,638,502,153
Gaps between scaffolds	0
Number of scaffolds	1,081
Scaffold N50	376,147,139
Scaffold L50	4
Number of contigs	3,530
Contig N50	3,661,507
Contig L50	366
Total number of chromosomes and plasmids	15
Number of component sequences (WGS or clone)	1,081

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	LR594632.1	=	NC_044031.1	0
Chromosome 2	LR594633.1	=	NC_044032.1	0
Chromosome 3	LR594634.1	=	NC_044033.1	0
Chromosome 4	LR594635.1	=	NC_044034.1	0
Chromosome 5	LR594636.1	=	NC_044035.1	0
Chromosome 6	LR594637.1	=	NC_044036.1	0
Chromosome 7	LR594638.1	=	NC_044037.1	0
Chromosome 8	LR594639.1	=	NC_044038.1	0
Chromosome 9	LR594640.1	=	NC_044039.1	0
Chromosome 10	LR594641.1	=	NC_044040.1	0
Chromosome 11	LR594642.1	=	NC_044041.1	0
Chromosome 12	LR594643.1	=	NC_044042.1	0
Chromosome 13	LR594644.1	=	NC_044043.1	0
Chromosome 14	LR594645.1	=	NC_044044.1	0
unplaced	n/a	n/a	n/a	1,066

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps
All	4,685,923,413	1,080	4,638,486,146	376,147,139	2,449
Chromosome 1	772,932,187	1	764,064,059	772,932,187	421
Chromosome 2	662,004,353	1	653,871,806	662,004,353	367
Chromosome 3	535,506,559	1	530,944,053	535,506,559	287
Chromosome 4	376,147,139	1	372,969,814	376,147,139	193
Chromosome 5	364,230,008	1	355,888,078	364,230,008	182
Chromosome 6	346,409,914	1	343,297,787	346,409,914	144
Chromosome 7	311,292,523	1	308,151,322	311,292,523	156
Chromosome 8	247,732,340	1	246,997,391	247,732,340	120
Chromosome 9	228,143,320	1	227,595,332	228,143,320	88
Chromosome 10	221,182,781	1	220,325,905	221,182,781	105
Chromosome 11	208,477,733	1	207,880,830	208,477,733	112
Chromosome 12	113,414,907	1	111,475,445	113,414,907	55
Chromosome 13	103,922,978	1	103,573,348	103,922,978	53
Chromosome 14	56,647,458	1	56,476,180	56,647,458	46
unplaced	137,879,213	1,066	134,974,796	165,730	120

Assembly

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aMicUni1.1

See Genome Information for Microcaecilia unicolor

Pathogen Detection Resources

There are 2 assemblies for this organism

History (Show revision history)

Comment

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Assembly Unit Name
Primary Assembly
non-nuclear