Bos taurus

BCM

• Genome Project

          #elem   min     max     mean    median  n50     sum
ctg       795203  1       63672   2844    1843    4184    2261840251
scf       449727  101     112430  5207    1463    13515   2341705768

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

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

Problems

Duplicates

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

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

Contaminants

                             #ctgs   min     max     mean    median  n50     total_bp
 UMD_Freeze2.0_contam        210657  71      840370  13709   1523    78508   2887902366
 UMD_Freeze2.0               187704  71      840370  15224   1609    79580   2857605192

 Chr   Ctg#    CtgLen    
 Chr1  4617    156423388
 Chr2  3468    137970877
 Chr3  3260    119903216
 Chr4  3032    120499176
 Chr5  3103    119907464
 Chr6  3570    116708387
 Chr7  3049    109835480
 Chr8  2954    110919444
 Chr9  2584    104153020
 Chr10 2712    103371818
 Chr11 2778    105871680
 Chr12 2673    88593048
 Chr13 2147    83426828
 Chr14 2549    84348855
 Chr15 2655    84608865
 Chr16 2547    80726864
 Chr17 1885    71868308
 Chr18 2195    65033181
 Chr19 1809    63177714
 Chr20 2146    70879996
 Chr21 1967    70124586
 Chr22 1628    60370627
 Chr23 1434    51154144
 Chr24 1380    61242035
 Chr25 1274    42287891
 Chr26 1668    51439476
 Chr27 1381    45311792
 Chr28 1186    45980408
 Chr29 1803    50592052
 ChrX  4883    136090029
 ChrU  113367  244784543
 -----------------------
 all  187704   2857605192

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

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