Bos taurus

BCM

• Genome Project

         #elem   min             max             mean            median          n50             sum
 contig  131620  91              326010          20755           10365           44270           2731814362
 placed  101579  91              250125          24286           13928           47485           2466971326
 chrom   30      44060403        161106243       87813777        84419198        106383598       2634413324

NCBI

• Genome Projects
• TA search

 SPECIES_CODE = "BOS TAURUS"                                                          37,788,710 traces
 SPECIES_CODE = "BOS TAURUS" and CENTER_NAME = "BCM"                                  35,596,825 traces
 
 SPECIES_CODE = "BOS TAURUS" and CENTER_NAME = "BCM" and TRACE_TYPE_CODE = "WGS"      24,863,627 traces
 SPECIES_CODE = "BOS TAURUS" and CENTER_NAME = "BCM" and TRACE_TYPE_CODE = "SHOTGUN"  10,716,306 traces
 SPECIES_CODE = "BOS TAURUS" and CENTER_NAME = "BCM" and TRACE_TYPE_CODE = "CLONEEND"     16,892 traces

Assembly

• Used UMDoverlapper to trim reads

          #elem       min     max     mean    median  n50     sum
 reads    35237868    68      1418    778     840     864     27406137041

Submission

• Genome Project
• WGS id (GPID): 32899

• Title: "A whole-genome assembly of the cow, Bos taurus"
• Authors:

 Steven Salzberg
 Aleksey Zimin
 Arthur Delcher
 Liliana Florea
 David Kelley
 Finian Hanrahan
 Guillaume Marcais
 Geo Pertea
 Michael Roberts
 Michael Schatz
 Curt Van Tassell
 James Yorke
 Poorani S.

• Assembler:

 Celera Assembler and UMD Overlapper.

• Sequencing Center :

 Baylor College of Medicine. 

• Source of DNA used for sequencing:

The source of the BAC library DNA was Hereford bull L1 Domino 99375, registration number 41170496. Dr. Michael MacNeil's laboratory, USDA-ARS, Miles City, MT provided the blood. The DNA for the whole genome shotgun sequences was provided by Dr. Timothy Smith's laboratory, U.S. Meat Animal Research Center, Clay Center, NE from white blood cells from L1 Dominette 01449, American Hereford Association registration number 42190680 (a daughter of L1 Domino 99375). A skin cell fibroblast cell line from the same animal is available from Dr. Carol Chitko-McKown's laboratory, although there is no sequence from that cell line.

• Sequence modifiers:

 [organism=Bos taurus][breed=Hereford][tech=wgs][chromosome=...]

• Submission: Use sequin

 /nfshomes/dpuiu/szdevel/sequin.8.10/sequin

• Sequence:

 Contig length summary:
           #seqs   min     max     mean    median  n50     sum
 all       210657  71      840370  13709   1523    78511   2887902366
 placed    75775   88      840370  34512   13416   88287   2615171268
 unplaced  134882  71      166670  2022    1322    1742    272731098

Duplicates

• Duplicate contigs : 111+2 : one copy was removed

 deg0003136509,7180003440308 : both unplaced
 deg0003084562,7180002954167 : both unplaced

Contaminants

Detected by NCBI (1st batch)

• list.exclude_contigs 4,814 ctgs (3,939 vector + 394 Ecoli + 452 other)
• list.trim_contigs 19,050 ctgs (18,336 vector + 289 Ecoli + 397 other)

Detected by NCBI (2nd batch)

• list.exclude_contigs 3 ctgs
• list.trim_contigs 46 ctgs

                             #ctgs   min     max     mean    median  n50     total_bp
 UMD_Freeze2.0_contam        210657  71      840370  13709   1523    78508   2887902366
 UMD_Freeze2.0               187683  71      840370  15225   1609    79580   2857554998

Files: /fs/szasmg3/dpuiu/bos_taurus/submission/decontam

Notes:

• The 4,814 ctgs were aligned to UniVec (-c 20 ; delta-filter -q)
  • 4,247 ctgs aligned to 89 vecto seqs
  • top ref hits:

 gnl|uv|J01749.1   Cloning vector pBR322
 gnl|uv|J01636.1   E.coli lactose operon with lacI, lacZ, lacY and lacA genes
 gnl|uv|AF102576.1 Cloning vector pSOS
 gnl|uv|L08959.1   pUC8 cloning vector 
 gnl|uv|L08931.1   pMAC7-8 cloning vector for site-directed mutagenesis
 gnl|uv|L09145.1   pUR222 cloning vector
 gnl|uv|U47102.2   Cloning vector pALTER<R>-Ex1
 ...

• The 4,814 ctgs were aligned to EcoliK12
  • 4,299 aligned 200bp+ to Ecoli
  • 3,877 aligned 100% to region 365521_365744 (224bp)

 >NC_000913.2_365521_365744 Escherichia coli K12, complete genome
 CATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATAC
 GAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTAA
 TTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAAT
 GAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGC

• The 4,814 ctgs were assembled based on 11,912 reads

 BCM          SHOTGUN    11247 (out of 10M reads)
 BCM          WGS        415   (out of 24M reads)
 NISC         SHOTGUN    213   (out of 0.7M reads)
 BARC         CLONEEND   14    ...
 BCM          CLONEEND   11
 BCCAGSC      CLONEEND   7
 TIGR         CLONEEND   4
 TIGR_JCVIJTC CLONEEND   1

• Avg UMD clipping rangeof the 11,912 reads is 840bp (vs 778 avg for the 3.53M assembled reads)

Local files

• Freeze dir files

 /fs/szasmg3/bos_taurus/Bos_taurus_UMD_2.0/contigs.unplaced.fa  : sequences
 /fs/szasmg3/bos_taurus/Bos_taurus_UMD_2.0/bos_taurus.agp       : all scaffolds

• Files uploaded

 Ftp server: ftp-private.ncbi.nlm.nih.gov
 Account: cbcb_trc
 Dir: uploads/
 Local files: /fs/szasmg3/dpuiu/bos_taurus/submission/ftp/   : 22 *sqn + 1 agp