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Information about assembly B73 RefGen_v1    (also known as AGPv1, B73 RefGen_v1)
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Genome Sequencing Project Information

   BAC by BAC sequencing and assembly of the B73 genome.
   GenBank BioProject   PRJNA10769  
   Project PI   Richard K Wilson
   Release date   2009
   Replaced by version   B73 RefGen_v2
   Funding   Sequencing the Maize Genome
   Browse Genome   Genome browser at MaizeGDB
   Data download   http://ftp.maizesequence.org/
   Publication status   published
Project reference The B73 Maize Genome: Complexity, Diversity, and Dynamics. Patrick S. Schnable, Doreen Ware, Robert S. Fulton, Joshua C. Stein, Fusheng Wei, Shiran Pasternak, Chengzhi Liang, Jianwei Zhang, Lucinda Fulton, Tina A. Graves, Patrick Minx, Amy Denise Reily, Laura Courtney, Scott S. Kruchowski, Chad Tomlinson, Cindy Strong, Kim Delehaunty, Catrina Fronick, Bill Courtney, Susan M. Rock, Eddie Belter, Feiyu Du, Kyung Kim, Rachel M. Abbott, Marc Cotton, Andy Levy, Pamela Marchetto, Kerri Ochoa, Stephanie M. Jackson, Barbara Gillam, Weizu Chen, Le Yan, Jamey Higginbotham, Marco Cardenas, Jason Waligorski, Elizabeth Applebaum, Lindsey Phelps, Jason Falcone, Krishna Kanchi, Thynn Thane, Adam Scimone, Nay Thane, Jessica Henke, Tom Wang, Jessica Ruppert, Neha Shah, Kelsi Rotter, Jennifer Hodges, Elizabeth Ingenthron, Matt Cordes, Sara Kohlberg, Jennifer Sgro, Brandon Delgado, Kelly Mead, Asif Chinwalla, Shawn Leonard, Kevin Crouse, Kristi Collura, Dave Kudrna, Jennifer Currie, Ruifeng He, Angelina Angelova, Shanmugam Rajasekar, Teri Mueller, Rene Lomeli, Gabriel Scara, Ara Ko, Krista Delaney, Marina Wissotski, Georgina Lopez, David Campos, Michele Braidotti, Elizabeth Ashley, Wolfgang Golser, HyeRan Kim, Seunghee Lee, Jinke Lin, Zeljko Dujmic, Woojin Kim, Jayson Talag, Andrea Zuccolo, Chuanzhu Fan, Aswathy Sebastian, Melissa Kramer, Lori Spiegel, Lidia Nascimento, Theresa Zutavern, Beth Miller, Claude Ambroise, Stephanie Muller, Will Spooner, Apurva Narechania, Liya Ren, Sharon Wei, Sunita Kumari, Ben Faga, Michael J. Levy, Linda McMahan, Peter Van Buren, Matthew W. Vaughn, Kai Ying, Cheng-Ting Yeh, Scott J. Emrich, Yi Jia, Ananth Kalyanaraman, An-Ping Hsia, W. Brad Barbazuk, Regina S. Baucom, Thomas P. Brutnell, Nicholas C. Carpita, Cristian Chaparro, Jer-Ming Chia, Jean-Marc Deragon, James C. Estill, Yan Fu, Jeffrey A. Jeddeloh, Yujun Han, Hyeran Lee, Pinghua Li, Damon R. Lisch, Sanzhen Liu, Zhijie Liu, Dawn Holligan Nagel, Maureen C. McCann, Phillip SanMiguel, Alan M. Myers, Dan Nettleton, John Nguyen, Bryan W. Penning, Lalit Ponnala, Kevin L. Schneider, David C. Schwartz, Anupma Sharma, Carol Soderlund, Nathan M. Springer, Qi Sun, Hao Wang, Michael Waterman, Richard Westerman, Thomas K. Wolfgruber, Lixing Yang, Yeisoo Yu, Lifang Zhang, Shiguo Zhou, Qihui Zhu, Jeffrey L. Bennetzen, R. Kelly Dawe, Jiming Jiang, Ning Jiang, Gernot G. Presting, Susan R. Wessler, Srinivas Aluru, Robert A. Martienssen, Sandra W. Clifton, W. Richard McCombie, Rod A. Wing, Richard K. Wilson
At MaizeGDB  
DOI  

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_v1
   Sequencing description   Sequencing technologies: Sanger
   Assembly description   Assembly methods: Sanger sequencing
Construction of pseudomolecules: Map-based order and orientation of a BAC tiling path.
   Browse Genome   Genome browser at MaizeGDB
   Data download   http://ftp.maizesequence.org/
   Release date   2009
   Sequencing method   Sanger
   Finishing strategy   Complete genome
   Genome coverage   4-6x
Assembly statistics
   N50 scaff length   1,260,849 bp
   N50 scaff count   496
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.
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   4a