Dbfetch

Dbfetch

ID   DAAA02000000; SV 02; linear; genomic DNA; SET; MAM; 75770 SQ.
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AC   DAAA02000000;
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PR   Project:PRJNA32899;
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DT   26-DEC-2021 (Rel. 144, Created)
DT   26-DEC-2021 (Rel. 144, Last updated, Version 0)
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DE   TPA: Bos taurus breed Hereford, whole genome shotgun sequence.
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KW   TPA; WGS; TPA:assembly; Third Party Data.
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OS   Bos taurus (cattle)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae;
OC   Bovinae; Bos.
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RN   [1]
RP   1-75770
RA   Zimin A.V., Delcher A.L., Florea L., Kelley D.R., Schatz M.C., Puiu D.,
RA   Hanrahan F., Pertea G., Van Tassell C.P., Sonstegard T.S., Marcais G.,
RA   Roberts M., Subramanian P., Yorke J.A., Salzberg S.L.;
RT   "A whole-genome assembly of the domestic cow, Bos taurus";
RL   Genome Biol. 10(4):R42(2009).
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RN   [2]
RC   Publication Status: Online-Only
RP   1-75770
RA   Merchant S., Wood D.E., Salzberg S.L.;
RT   "Unexpected cross-species contamination in genome sequencing projects";
RL   Peerj 2:E675(2014).
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RN   [3]
RP   1-75770
RA   Salzberg S.L., Zimin A., Delcher A., Florea L., Kelley D., Hanrahan F.,
RA   Marcais G., Pertea G., Puiu D., Roberts M., Schatz M., Van Tassell C.,
RA   Yorke J.C., Subramanian P.J.;
RT   ;
RL   Submitted (19-DEC-2008) to the INSDC.
RL   Center for Bioinformatics and Computational Biology, University of
RL   Maryland, 3115 Biomolecular Sciences Building, College Park, MD 20742, USA
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RN   [4]
RP   1-75770
RA   Salzberg S.L., Zimin A., Delcher A., Florea L., Kelley D., Hanrahan F.,
RA   Marcais G., Pertea G., Puiu D., Roberts M., Schatz M., Van Tassell C.,
RA   Yorke J.C., Poorani S.J.;
RT   ;
RL   Submitted (24-AUG-2009) to the INSDC.
RL   Center for Bioinformatics and Computational Biology, University of
RL   Maryland, 3115 Biomolecular Sciences Building, College Park, MD 20742, USA
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DR   BioSample; SAMN02898106.
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CC   On Sep 1, 2009 this sequence version replaced gi:256352173.
CC   The Bos taurus whole genome shotgun (WGS) project has the project
CC   accession DAAA00000000.  This version of the project (02) has the
CC   accession number DAAA02000000, and consists of sequences
CC   DAAA02000001-DAAA02075770.
CC   This assembly of the Bos taurus genome was created from the traces
CC   of BioProject PRJNA12555.  This assembly closes thousands of gaps
CC   and corrects many inversions, deletions, translocations and
CC   single-nucleotide errors that were present on other assemblies, as
CC   determined by alignment to independent mapping data and to
CC   independently sequenced transcripts (full-length cDNAs). In this
CC   assembly synteny between the cow and human genomes and independent
CC   mapping data were used to assemble roughly 99% of the genome onto
CC   the 30 Bos taurus chromosomes.
CC   Bos_taurus_UMD3.1 (UMD3.1) is an update to the UMD3 assembly that
CC   corrects errors in the gap types. The gap type changes join many
CC   placed scaffolds together but do not change the sequences of the
CC   chromosomes or the sequences of the unplaced scaffolds.
CC   Annotation was produced by the NCBI Eukaryotic Genomes Annotation
CC   Pipeline Group using Gnomon, and added to the scaffolds in May
CC   2010.
CC   In June 2014 138 contigs were suppressed because they are
CC   contaminants, so the assembly name was updated to
CC   Bos_taurus_UMD_3.1.1, assembly GCA_000003055.4.
CC   In November 2014 37 more contigs were suppressed because they are
CC   contaminants and two contigs (DAAA02065100 and DAAA02065112) were
CC   unsuppressed because they were determined to be Bos taurus.
CC   Therefore, a total of 173 contigs are suppressed. The assembly name
CC   remains Bos_taurus_UMD_3.1.1 but the assembly was incremented to
CC   GCA_000003055.5.
CC   
CC   ##Genome-Assembly-Data-START##
CC   Assembly Method       :: UMD Overlapper v. 2009; additional
CC   processing
CC   Assembly Name         :: Bos_taurus_UMD_3.1.1
CC   Genome Coverage       :: 9x
CC   Sequencing Technology :: Sanger
CC   ##Genome-Assembly-Data-END##
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FH   Key             Location/Qualifiers
FH
FT   source          1..75770
FT                   /organism="Bos taurus"
FT                   /mol_type="genomic DNA"
FT                   /sex="pooled male and female"
FT                   /tissue_type="blood"
FT                   /note="breed: Hereford"
FT                   /db_xref="taxon:9913"
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WGS  DAAA02000001-DAAA02075770
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CON  GK000001-GK000030;GJ060423-GJ063645;GJ057137-GJ060422
//