Bos taurus
BCM
NCBI
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
210657 contigs originally
All:
#elem min max mean median n50 sum unplaced placed list.exclude_contigs(ctgs) 4813 316 16661 1511 1485 1514 7271697 4801 12 list.trim_contigs(ctgs) 19049 457 433546 4424 1204 70673 84270091 16631 2418 list.trim_contigs(regions) 30279 48 2479 354 319 445 10724357 . .
Exclude: 4813 DELETED
#elem min max mean median n50 sum unplaced placed all 4813 316 16661 1511 1485 1514 7271697 4801 12 all DELETED mitochondrion 73 1003 2081 1368 1299 1390 99872 73 0 degenerates 43 316 1098 842 872 889 36201 38 5 contaminants 4697 861 16661 1519 1487 1517 7135624 4690 7
Trim: 17870 DELETED
#elem min max mean median n50 sum unplaced placed all 19049 457 433546 4424 1204 70673 84270091 16631 2418 2000- 17870 457 1995 1234 1188 1224 22044745 16448 1422 all DELETED 2000+ 1179 2004 433546 52778 28023 112295 62225346 183 996 some DELETED
Trim 2000+ vector in the middle: 7+4+6=17 DELETED , 4*2+6*2=20 ADDED
#elem min max mean median n50 sum unplaced placed all 24 2190 274661 64464 20588 162585 1547139 8 16 deleted 7 2190 3246 2667 2654 2654 18668 6 1 all DELETED trimmed 7 4182 162585 53460 20588 102303 374220 2 5 replaced_by_2 4 35208 224013 113166 143258 143258 452665 0 4 join100004686,join100006091,join100007519,join100007923 split_into_2 6 5365 274661 116931 149360 227489 701586 0 6 7180003327752,7180003312564,7180003340990,7180003313669,7180003378076,7180003341221
=> 210657-4813-17870-7+10=187977
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