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Information about assembly B73 RefGen_v3    (also known as AGPv3, B73 RefGen_v3)
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Genome Sequencing Project Information

   To fill in gaps in the B73_v2 assembly via WGS and contig re-orientation via Sorghum-guided synteny
   GenBank BioProject   PRJNA72137  
   Project PI   Doreen Ware
   Project start date   2013-01-01
   Release date   2013
   Changes to previous version   500 fosmid clones were sequenced and finished and an 8x shotgun sequence was generated via 454 sequencing. BAC assemblies were improved for BACs in the tiling path, and gaps in v2 were filled with resultant sequence contigs.
   Replaced by version   Zm-B73-REFERENCE-GRAMENE-4.0
   Funding   NSF: Improving the Sequence of the Maize Genome
   Browse Genome   Genome browser at MaizeGDB
   Data download   ftp://ftp.ensemblgenomes.org/pub/plants/release-22/fasta/zea_mays/dna
Project reference A panoply of genomics techniques to update the Zea mays B73 reference sequence and annotations. Andrew J. Olson, Joshua C. Stein, Shiran Pasternak, Jeffrey C. Glaubitz, Edward S. Buckler, Fusheng Wei, Jianwei Zhang, Rod A. Wing, Robert S. Fulton, Richard K. Wilson, Ethalinda K.S. Cannon, Carson M. Andorf, Carolyn J. Lawrence

Stock and Biosample Information

Stock information
   Stock name   Coe PI 550473
   Stock record   47638
   Stock details   Coe PI 550473
Biosample information
   GenBank BioSample   SAMN02981394  
   Sample description   The source for the inbred line B73 used to make the BAC libraries that were sequenced is available from the North Central Regional Plant Introduction Station through the U.S. National Plant Germplasm System under the accession PI 550473. When requesting seed from the North Central Regional Plant Introduction Station, ask for any lot descended from the Coe PI 550473 lines.

Sequencing and Assembly Information

   Assembly name   B73 RefGen_v3
   Sequencing description   Sequencing technologies: Sanger and 454
   Assembly description   Assembly methods: phredPhrap v. 2009 and ABySS v. 1.2.7 and
Construction of pseudomolecules: Map-based order and orientation of a BAC tiling path, with some gaps filled with 454 contigs.
   Browse Genome   Genome browser at MaizeGDB
   Data download   ftp://ftp.ensemblgenomes.org/pub/plants/release-22/fasta/zea_mays/dna
   Release date   2013
   Sequencing method   Sanger and 454
   Finishing strategy   Complete genome
   Genome coverage   6x
   Seq service provider   Roche
Assembly statistics
   Scaff num   523
   N50 scaff length   8,225,948 bp
   N50 scaff count   79
   N90 scaff length   595,319 bp
   N90 scaff count   366
   N50 contig length   13,961 bp
   N50 contig count   41,305
Total number of scaffolds in assembly.
The length of scaffold which takes the sum length (summing from longest to shortest scaffold) past 50% of the total assembly size.
How many scaffolds are counted in reaching the N50 threshold.
The length of scaffold which takes the sum length (summing from longest to shortest scaffold) past 90% of the total assembly size.
How many scaffolds are counted in reaching the N90 threshold.
The length of contig which takes the sum length (summing from longest to shortest contig) past 50% of the total assembly size.
How many contig are counted in reaching the N50 threshold.
A contig is a contiguous consensus sequence that is derived from a collection of overlapping reads.
A scaffold is set of a ordered and orientated contigs that are linked to one another by mate pairs of sequencing reads.

Annotation

   Annotation Identifier   5b+