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Source database (GenBank or RefSeq) File type

Btau_5.0.1

Organism name:

Bos taurus (cattle)

Infraspecific name:

Breed: Hereford

Sex:

pooled male and female

BioSample:

SAMN02898106

BioProject:

PRJNA12555

Submitter:

Cattle Genome Sequencing International Consortium

Date:

2015/11/19

Assembly level:

Chromosome

Genome representation:

full

Excluded from RefSeq:

superseded by newer assembly for species

GenBank assembly accession:

GCA_000003205.6 (latest)

RefSeq assembly accession:

GCF_000003205.7 (suppressed) see latest RefSeq assembly for this species

RefSeq assembly and GenBank assembly identical:

yes

WGS Project:

AAFC05

Assembly method:

UMD Overlapper v. 2009; additional processing + PBJelly2 v. 14.9.9

Genome coverage:

19.0x

Sequencing technology:

Sanger; PacBio RS II

IDs: 585021 [UID] 2689988 [GenBank] 2701278 [RefSeq]

See Genome Information for Bos taurus

Pathogen Detection Resources

There are 26 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_000003205.6	=	GCF_000003205.7	Btau_5.0.1	Chromosome	Latest GenBank, RefSeq suppressed
GCA_000003205.5	n/a	n/a	Btau_5.0	Chromosome	Replaced GenBank
GCA_000003205.4	=	GCF_000003205.5	Btau_4.6.1	Chromosome	Replaced GenBank, RefSeq suppressed
GCA_000003205.3	n/a	n/a	Btau_4.6	Chromosome	Replaced GenBank
GCA_000003205.2	≠	GCF_000003205.4	Btau_4.2	Chromosome	Replaced GenBank, RefSeq suppressed
GCA_000003205.1	=	GCF_000003205.3	Btau_4.2	Chromosome	Replaced GenBank, RefSeq suppressed
n/a	n/a	GCF_000003205.2	Btau_4.0	Chromosome	RefSeq suppressed
n/a	n/a	GCF_000003205.1	Btau_3.1	Chromosome	RefSeq suppressed

Comment

This version of the genome has 7x coverage and covers 95% of the genome. It was assembled from the pooled reads of BACs and whole genome shotgun sequences so is from two cattle (L1 Domino 99375 and L1 Dominette ... 01449). Some of the BACs were sequenced individually and some were sequenced using a pooling method.
Assembly Btau_4.6.1 has an improved version of chromosome Y compared to assembly Btau_4.6, which was a reassembly to replace some WGS sequences with BAC sequences and to add some WGS sequences from the AAFC02000000 version of the WGS project that were not included in the current version, AAFC03000000.  more

Global statistics

Total sequence length	2,724,980,740
Total ungapped length	2,713,032,866
Gaps between scaffolds	2,856
Number of scaffolds	5,998
Scaffold N50	6,806,220
Scaffold L50	104
Number of contigs	42,267
Contig N50	276,285
Contig L50	2,849
Total number of chromosomes and plasmids	31
Number of component sequences (WGS or clone)	42,574

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	CM000177.6	=	NC_007299.6	0
Chromosome 2	CM000178.7	=	NC_007300.6	0
Chromosome 3	CM000179.6	=	NC_007301.6	0
Chromosome 4	CM000180.6	=	NC_007302.6	0
Chromosome 5	CM000181.7	=	NC_007303.6	0
Chromosome 6	CM000182.7	=	NC_007304.6	0
Chromosome 7	CM000183.7	=	NC_007305.6	0
Chromosome 8	CM000184.6	=	NC_007306.6	0
Chromosome 9	CM000185.7	=	NC_007307.6	0
Chromosome 10	CM000186.6	=	NC_007308.6	0
Chromosome 11	CM000187.6	=	NC_007309.6	0
Chromosome 12	CM000188.7	=	NC_007310.6	0
Chromosome 13	CM000189.7	=	NC_007311.6	0
Chromosome 14	CM000190.6	=	NC_007312.6	0
Chromosome 15	CM000191.7	=	NC_007313.6	0
Chromosome 16	CM000192.5	=	NC_007314.5	0
Chromosome 17	CM000193.6	=	NC_007315.6	0
Chromosome 18	CM000194.7	=	NC_007316.6	0
Chromosome 19	CM000195.6	=	NC_007317.6	0
Chromosome 20	CM000196.6	=	NC_007318.6	0
Chromosome 21	CM000197.6	=	NC_007319.6	0
Chromosome 22	CM000198.6	=	NC_007320.6	0
Chromosome 23	CM000199.8	=	NC_007324.6	0
Chromosome 24	CM000200.7	=	NC_007325.6	0
Chromosome 25	CM000201.6	=	NC_007326.6	0
Chromosome 26	CM000202.7	=	NC_007327.6	0
Chromosome 27	CM000203.6	=	NC_007328.5	0
Chromosome 28	CM000204.6	=	NC_007329.6	0
Chromosome 29	CM000205.6	=	NC_007330.6	0
Chromosome X	CM000206.6	=	NC_007331.5	0
Chromosome Y	CM001061.2	=	NC_016145.1	0
unplaced	n/a	n/a	n/a	3,112

Molecule	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps	Unspanned Gaps
All	2,724,980,740	5,998	2,713,032,866	6,806,220	36,269	2,856
Chromosome 1	158,972,876	93	158,695,025	7,156,122	1,701	92
Chromosome 2	137,479,425	57	137,248,860	12,146,345	1,281	56
Chromosome 3	121,888,057	60	121,684,121	11,414,096	1,231	59
Chromosome 4	121,284,772	72	121,066,657	5,799,018	1,322	71
Chromosome 5	121,584,146	113	121,343,079	4,968,909	1,334	112
Chromosome 6	119,927,886	124	119,589,815	5,011,317	2,039	123
Chromosome 7	113,155,487	186	111,887,445	3,094,268	1,207	185
Chromosome 8	114,055,384	288	113,806,092	2,257,312	1,427	287
Chromosome 9	106,206,484	376	105,986,648	1,310,995	1,132	375
Chromosome 10	104,654,538	44	104,450,394	14,233,401	1,254	43
Chromosome 11	107,582,167	49	107,405,563	17,955,530	1,018	48
Chromosome 12	91,593,655	178	91,359,435	7,019,983	1,162	177
Chromosome 13	84,590,997	31	84,430,449	16,386,421	1,024	30
Chromosome 14	85,007,120	87	84,754,767	14,754,064	1,746	86
Chromosome 15	85,681,136	61	85,322,782	8,221,776	976	60
Chromosome 16	82,000,027	35	81,803,502	12,767,545	1,047	34
Chromosome 17	75,367,154	49	75,210,535	8,802,906	852	48
Chromosome 18	66,346,785	51	66,155,795	8,231,141	1,155	50
Chromosome 19	64,325,510	43	64,170,860	4,842,069	950	42
Chromosome 20	72,301,449	39	72,189,598	5,729,197	695	38
Chromosome 21	71,883,091	29	71,727,291	10,915,954	997	28
Chromosome 22	61,679,430	20	61,586,469	17,175,872	517	19
Chromosome 23	52,684,911	67	52,584,888	9,227,632	531	66
Chromosome 24	62,911,103	15	62,806,310	24,978,401	612	14
Chromosome 25	43,100,425	19	43,011,682	12,083,132	629	18
Chromosome 26	51,889,111	22	51,794,119	7,692,611	604	21
Chromosome 27	45,695,690	56	45,457,327	4,534,909	842	55
Chromosome 28	46,481,278	24	46,400,409	8,381,507	477	23
Chromosome 29	51,869,468	48	51,707,305	4,488,817	757	47
Chromosome X	150,266,161	538	149,460,727	3,503,835	5,745	537
Chromosome Y	43,300,181	12	38,720,081	10,947,484	5	12
unplaced	9,214,836	3,112	9,214,836	5,677	0	0

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Btau_5.0.1

See Genome Information for Bos taurus

Pathogen Detection Resources

There are 26 assemblies for this organism

History (Show revision history)

Comment

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