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Information about assembly 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 start date   2013-01-01
   Browse Genome   Genome browser at MaizeGDB
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 details   Coe PI 550473
   Stock provided by   North Central Regional Plant Introduction Station
Biosample information
   Sample description   Coe PI 550473
   Collection date   1-Jan-05
   Collected by   Jack Gardiner

Sequencing and Assembly Information

   Assembly name   B73 RefGen_v3
   Sequencing description  
   Assembly description   A complementary set of whole genome shotgun (WGS) sequencing reads derived from the same samples were used to recover some of the missing gene space. Novel contigs were selected from de novo assemblies of the WGS data based on alignments to full length cDNAs and guided into gaps in the assembly based on genetic mapping and synteny with rice and Sorghum. This synteny-refined genetic map was also used to place five previously unanchored BAC clones and to reposition three other BACs. These changes were integrated into a new version of the reference assembly, B73 RefGen_v3, along with new and updated gene models. Furthermore, the RefGen_v3 assembly was used to update the order and orientation of contigs within 15,832 of the 16,082 BAC sequence records in GenBank

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   Browse Genome   Genome browser at MaizeGDB
   Finishing strategy   To improve the B73 assembly. 14x coverage, 126677 contigs
   Genome coverage   14X
   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.