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Ruth Westervelt
one millionrice snp array
Design & Status
McCouch RiceLab Department of Plant Breeding & Genetics
Cornell University
© 2015 McCouch RiceLab
backgroundThe original NSF-TV grant was funded to develop a 10k fixed array with Illumina Technology.
Affymetrix technology offered 44k (minimum) but only guaranteed at least 50% conversion rate. Still, this was double what we could afford with Illumina.
OryzaSNP Perlegen resequencing of 20 lines (no wilds, only 1 aromatic, only 25% of the genome interrogated).
OMAP BAC-end sequence alignments (Rod Wing)—additional SNPs to fill in regions not covered by OryzaSNP.
snp discovery
© 2015 McCouch RiceLab
Reference Sequence
Raw Data Multiple FASTQ Files
Hierarchical Reference Index
panati
Genome Coverage and Detected
Variations
Diploid Genotype
Matrix
Mapping and Alignment Realignment Variant
DetectionSNP/Genotype
Calling
index generation primary analysis secondary analysis
Index Generation
Short Read Analysis Tool
rice diversity panelBroad Geographic and Morphological of Rice Diversity
Indica Aus
© 2015 McCouch RiceLab
Japonica Aromatic
Temperate Japonica
Tropical Japonica
Indica Indica
This presentation © 2013 RuthWestervelt
Toward a Rhetoric of Environmental Visualization
Ruth WesterveltEnvironmental & Interior
Design Program