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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.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix134

Accessions (data included in GigaDB):

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

Keywords:

zea mays sequencing haplotype map genotyping variant discovery linkage disequilibrium identity by descent imputation 

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
282set_CM105381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CM105
Alternative accession-BioProject:PRJNA389800
...
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282set_CM174381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CM174
Alternative accession-BioProject:PRJNA389800
...
+
282set_CM37381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CM37
Alternative accession-BioProject:PRJNA389800
...
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282set_CM7381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CM7
Alternative accession-BioProject:PRJNA389800
...
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282set_CML10381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML10
Alternative accession-BioProject:PRJNA389800
...
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282set_CML103381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML103
Alternative accession-BioProject:PRJNA389800
...
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282set_CML108381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML108
Alternative accession-BioProject:PRJNA389800
...
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282set_CML11381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML11
Alternative accession-BioProject:PRJNA389800
...
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282set_CML14381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML14
Alternative accession-BioProject:PRJNA389800
...
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282set_CML154Q381124maysZea mays sub sp. Mays Description:DNA extracted from Mays cultivar 282se...
Cultivar:282set_CML154Q
Alternative accession-BioProject:PRJNA389800
...
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Displaying 61-70 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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