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Source database (GenBank or RefSeq) File type

VicPac3.1

This assembly has been replaced. See current version

Anomalous assembly.

Organism name:

Vicugna pacos (alpaca)

Isolate:

Carlotta (AHFN-0088)

Sex:

female

BioSample:

SAMN01096418

BioProject:

PRJNA544883

Submitter:

Deakin University

Date:

2019/07/15

Assembly level:

Scaffold

Genome representation:

full

Assembly anomaly:

contaminated

Excluded from RefSeq:

contaminated

GenBank assembly accession:

GCA_000164845.4 (replaced)

RefSeq assembly accession:

GCF_000164845.3 (replaced)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in RefSeq: chromosome MT

Data displayed for RefSeq version

WGS Project:

ABRR03

Assembly method:

MaSuRCA, Metassembler, DoveTail HiRise v. JUN-17

Expected final version:

yes

Reference guided assembly:

GCA_000164845.3; GCF_000164845.2

Genome coverage:

260.0x

Sequencing technology:

Illumina HiSeq; PacBio RSII; Dovetail genomics

IDs: 3848621 [UID] 12130838 [GenBank] 12983738 [RefSeq]

See Genome Information for Vicugna pacos

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_000164845.5	≠	GCF_000164845.4	VicPac3.2	Scaffold	Latest GenBank, Latest RefSeq
GCA_000164845.4	≠	GCF_000164845.3	VicPac3.1	Scaffold	Replaced GenBank, Replaced RefSeq
GCA_000164845.3	≠	GCF_000164845.2	Vicugna_pacos-2.0.2	Scaffold	Replaced GenBank, Replaced RefSeq
GCA_000164845.2	≠	GCF_000164845.1	Vicugna_pacos-2.0.1	Scaffold	Replaced GenBank, Replaced RefSeq
GCA_000164845.1	n/a	n/a	VicPac1.0	Scaffold	Replaced GenBank

Comment

In May 2022 1 sequence was suppressed because it was found to be a contaminant.

Global statistics

Total sequence length	2,119,617,549
Total ungapped length	2,031,198,268
Gaps between scaffolds	0
Number of scaffolds	77,390
Scaffold N50	24,022,313
Scaffold L50	25
Number of contigs	243,670
Contig N50	29,536
Contig L50	18,008
Total number of chromosomes and plasmids	38
Number of component sequences (WGS or clone)	77,390

Molecule	Sequence Role	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps	Unspanned Gaps
All	Assembled molecule	2,119,600,897	77,389	2,031,181,616	24,022,313	166,280	0
Chromosome 1	AllAssembled moleculeUnlocalized scaffolds	101,041,2330101,041,233	505	97,812,416097,812,416	27,143,056027,143,056	7,18907,189	000
Chromosome 2	AllAssembled moleculeUnlocalized scaffolds	121,370,6200121,370,620	101	117,484,2540117,484,254	121,370,6200121,370,620	9,20509,205	000
Chromosome 3	AllAssembled moleculeUnlocalized scaffolds	83,363,794083,363,794	303	80,817,439080,817,439	65,747,404065,747,404	5,93405,934	000
Chromosome 4	AllAssembled moleculeUnlocalized scaffolds	65,636,945065,636,945	303	63,756,833063,756,833	43,451,823043,451,823	3,95603,956	000
Chromosome 5	AllAssembled moleculeUnlocalized scaffolds	96,274,254096,274,254	101	93,479,546093,479,546	96,274,254096,274,254	6,75206,752	000
Chromosome 6	AllAssembled moleculeUnlocalized scaffolds	74,791,714074,791,714	202	72,762,768072,762,768	63,770,147063,770,147	4,11804,118	000
Chromosome 7	AllAssembled moleculeUnlocalized scaffolds	31,168,711031,168,711	101	30,244,708030,244,708	31,168,711031,168,711	2,06902,069	000
Chromosome 8	AllAssembled moleculeUnlocalized scaffolds	70,270,077070,270,077	101	68,336,020068,336,020	70,270,077070,270,077	4,65504,655	000
Chromosome 9	AllAssembled moleculeUnlocalized scaffolds	53,761,482053,761,482	303	52,165,586052,165,586	30,167,013030,167,013	3,32103,321	000
Chromosome 10	AllAssembled moleculeUnlocalized scaffolds	39,582,034039,582,034	101	38,395,188038,395,188	39,582,034039,582,034	2,62602,626	000
Chromosome 11	AllAssembled moleculeUnlocalized scaffolds	74,979,631074,979,631	505	72,291,087072,291,087	18,667,169018,667,169	5,18805,188	000
Chromosome 12	AllAssembled moleculeUnlocalized scaffolds	48,986,614048,986,614	202	47,417,673047,417,673	48,142,004048,142,004	3,58503,585	000
Chromosome 13	AllAssembled moleculeUnlocalized scaffolds	61,008,235061,008,235	303	59,246,871059,246,871	18,253,595018,253,595	4,02404,024	000
Chromosome 14	AllAssembled moleculeUnlocalized scaffolds	67,111,318067,111,318	202	64,513,462064,513,462	36,104,741036,104,741	5,44105,441	000
Chromosome 15	AllAssembled moleculeUnlocalized scaffolds	32,418,436032,418,436	202	31,401,654031,401,654	31,125,524031,125,524	2,18902,189	000
Chromosome 16	AllAssembled moleculeUnlocalized scaffolds	39,074,364039,074,364	606	37,664,811037,664,811	24,459,858024,459,858	2,74502,745	000
Chromosome 17	AllAssembled moleculeUnlocalized scaffolds	46,944,759046,944,759	101	45,673,032045,673,032	46,944,759046,944,759	2,93202,932	000
Chromosome 18	AllAssembled moleculeUnlocalized scaffolds	29,910,177029,910,177	202	28,860,801028,860,801	17,793,591017,793,591	2,12102,121	000
Chromosome 19	AllAssembled moleculeUnlocalized scaffolds	24,022,313024,022,313	101	23,368,720023,368,720	24,022,313024,022,313	1,26001,260	000
Chromosome 20	AllAssembled moleculeUnlocalized scaffolds	38,741,345038,741,345	202	37,408,731037,408,731	21,123,902021,123,902	2,78002,780	000
Chromosome 21	AllAssembled moleculeUnlocalized scaffolds	29,520,914029,520,914	303	28,601,971028,601,971	11,290,377011,290,377	2,12902,129	000
Chromosome 22	AllAssembled moleculeUnlocalized scaffolds	25,522,599025,522,599	101	24,665,082024,665,082	25,522,599025,522,599	1,83301,833	000
Chromosome 23	AllAssembled moleculeUnlocalized scaffolds	29,440,657029,440,657	202	28,825,992028,825,992	26,462,452026,462,452	1,44001,440	000
Chromosome 24	AllAssembled moleculeUnlocalized scaffolds	18,346,407018,346,407	101	17,773,441017,773,441	18,346,407018,346,407	1,29501,295	000
Chromosome 25	AllAssembled moleculeUnlocalized scaffolds	60,195,357060,195,357	303	58,098,863058,098,863	20,942,430020,942,430	4,56204,562	000
Chromosome 26	AllAssembled moleculeUnlocalized scaffolds	27,987,978027,987,978	202	26,966,820026,966,820	15,017,617015,017,617	2,48302,483	000
Chromosome 27	AllAssembled moleculeUnlocalized scaffolds	22,699,463022,699,463	101	21,987,411021,987,411	22,699,463022,699,463	1,53501,535	000
Chromosome 28	AllAssembled moleculeUnlocalized scaffolds	16,162,605016,162,605	101	15,573,339015,573,339	16,162,605016,162,605	1,31101,311	000
Chromosome 29	AllAssembled moleculeUnlocalized scaffolds	26,137,040026,137,040	202	25,120,907025,120,907	14,278,588014,278,588	2,27302,273	000
Chromosome 30	AllAssembled moleculeUnlocalized scaffolds	13,130,742013,130,742	303	12,636,419012,636,419	9,688,54009,688,540	1,04901,049	000
Chromosome 31	AllAssembled moleculeUnlocalized scaffolds	13,602,737013,602,737	101	13,059,931013,059,931	13,602,737013,602,737	1,15001,150	000
Chromosome 32	AllAssembled moleculeUnlocalized scaffolds	22,732,685022,732,685	303	21,809,606021,809,606	20,187,997020,187,997	1,75301,753	000
Chromosome 33	AllAssembled moleculeUnlocalized scaffolds	16,261,182016,261,182	101	15,689,090015,689,090	16,261,182016,261,182	1,23501,235	000
Chromosome 34	AllAssembled moleculeUnlocalized scaffolds	22,097,801022,097,801	101	21,329,119021,329,119	22,097,801022,097,801	1,76601,766	000
Chromosome 35	AllAssembled moleculeUnlocalized scaffolds	18,484,027018,484,027	404	17,321,731017,321,731	6,682,74406,682,744	1,91801,918	000
Chromosome 36	AllAssembled moleculeUnlocalized scaffolds	5,377,76505,377,765	303	4,677,26004,677,260	2,828,35102,828,351	9810981	000
Chromosome X	AllAssembled moleculeUnlocalized scaffolds	34,309,508034,309,508	707	33,003,848033,003,848	6,359,22806,359,228	2,07002,070	000
unplaced	Assembled molecule	517,133,374	77,303	480,939,186	6,680,802	53,407	0

Assembly

Genome Assembly

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VicPac3.1

See Genome Information for Vicugna pacos

Pathogen Detection Resources

There are 3 assemblies for this organism

History (Show revision history)

Comment

Global statistics

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Assembly Information

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Global assembly definition

Assembly statistics

Assembly Unit Name
Primary Assembly
non-nuclear