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Data released on December 27, 2017

Supporting data for "Construction of the third generation Zea mays haplotype map"

Bukowski, R; Guo, X; Lu, Y; Zou, C; He, B; Rong, Z; Wang, B; Xu, D, X; Yang, B; Xie, C; Fan, L; Gao, S; Xu, X; Zhang, G; Li, Y; Jiao, Y; Doebley, J; Ross-Ibarra, J; Lorant, A; Buffalo, V; Romay , M, C; Buckler , E, S; , Y, X; Ware, D; Lai, J; Sun, Q (2017): Supporting data for "Construction of the third generation Zea mays haplotype map" GigaScience Database. http://dx.doi.org/10.5524/100339 RIS BibTeX Text

Characterization of genetic variations in maize has been challenging, mainly due to deterioration of collinearity between individual genomes in the species. An international consortium of maize research groups combined resources to develop the maize haplotype version 3 (HapMap 3), built from whole genome sequencing data from 1,218 maize lines, covering pre-domestication and domesticated Zea mays varieties across the world. A new computational pipeline was set up to process over 12 trillion bp of sequencing data, and a set of population genetics filters were applied to identify over 83 million variant sites. We identified polymorphisms in regions where collinearity is largely preserved in the maize species. However, the fact that the B73 genome used as the reference only represents a fraction of all haplotypes is still an important limiting factor.

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Related manuscripts:

doi:10.1093/gigascience/gix134

Accessions (data included in GigaDB):

BioProject: PRJNA389800
BioProject: PRJNA260788
BioProject: PRJNA399729
BioProject: PRJNA82843
SRA: SRA051245

Genomic

http://gigadb.org/images/data/cropped/100339.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
hmp3_TIL1176912Balsas teosinte Zea mays subsp. parviglumis Description:DNA extracted from Mays cultivar TIL11
Cultivar:TIL11
Alternative accession-BioProject:PRJNA399729
...
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hmp3_TIL25-TIP48976912Balsas teosinte Zea mays subsp. parviglumis Description:DNA extracted from Mays cultivar TIL25...
Cultivar:TIL25-TIP489
Alternative accession-BioProject:PRJNA399729
...
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hmp3_TIL0976912Balsas teosinte Zea mays subsp. parviglumis Description:DNA extracted from Mays cultivar TIL09
Cultivar:TIL09
Alternative accession-BioProject:PRJNA399729
...
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hmp3_TIL1076912Balsas teosinte Zea mays subsp. parviglumis Description:DNA extracted from Mays cultivar TIL10
Cultivar:TIL10
Alternative accession-BioProject:PRJNA399729
...
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hmp3_TIL14-TIP49876912Balsas teosinte Zea mays subsp. parviglumis Description:DNA extracted from Mays cultivar TIL14...
Cultivar:TIL14-TIP498
Alternative accession-BioProject:PRJNA399729
...
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hmp3_TIL1576912Balsas teosinte Zea mays subsp. parviglumis Description:DNA extracted from Mays cultivar TIL15
Cultivar:TIL15
Alternative accession-BioProject:PRJNA399729
...
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hmp3_TIL0376912Balsas teosinte Zea mays subsp. parviglumis Description:DNA extracted from Mays cultivar TIL03
Cultivar:TIL03
Alternative accession-BioProject:PRJNA399729
...
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hmp3_TIL0576912Balsas teosinte Zea mays subsp. parviglumis Description:DNA extracted from Mays cultivar TIL05
Cultivar:TIL05
Alternative accession-BioProject:PRJNA399729
...
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TIL0176912Balsas teosinte Zea mays subsp. parviglumis Description:DNA extracted from Mays cultivar TIL01
Cultivar:TIL01
Alternative accession-BioProject:SRA051245
...
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hmp3_TIL01-JD76912Balsas teosinte Zea mays subsp. parviglumis Description:DNA extracted from Mays cultivar TIL01...
Cultivar:TIL01-JD
Alternative accession-BioProject:PRJNA399729
...
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Displaying 1-10 of 1282 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
archivezip187.13 MB2017-12-22
SNPsVCF2.01 GB2017-11-03
SNPsVCF4.25 GB2017-11-03
SNPsVCF4.07 GB2017-11-03
SNPsVCF4.21 GB2017-11-03
SNPsVCF9.03 GB2017-11-03
SNPsVCF8.62 GB2017-11-03
SNPsVCF3.22 GB2017-11-03
SNPsVCF6.87 GB2017-11-03
SNPsVCF6.41 GB2017-11-03
Displaying 1-10 of 52 File(s).

History:

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