Sequence Data
Whole genome sequencing data used to build haplotype maps and genome assemblies.
HapMap 3.2.1 whole genome sequencing data
Alignments to the maize B73 reference genome v3, generated with bwa mem, with BAM index files from samtools index. If you need FASTQ files, the SamToFastq tool in Picard converts BAM to FASTQ.
The file gateway no longer links to these BAM files. Email qisun@cornell.edu for access.
View this data set on the Panzea file gatewayMaize 282 association panel
Whole genome sequencing data in both FASTQ and BAM formats. Genotype calls derived from these data are on the Genotypes page.
View this data set on the Panzea file gatewayCML247
Five PCR-free libraries sequenced for CML247 at 130X in total: a 500 bp library (~65X, 2×300 bp, 10 MiSeq lanes), an 800 bp library (~17X, 2×150 bp, 1 HiSeq 2500 lane), and 3–5 kb, 5–7 kb, and 8–10 kb mate-pair libraries (each ~17X, 2×150 bp, 1 HiSeq 2500 lane).
The file gateway does not link to these reads. Email qisun@cornell.edu for access.
View this data set on the Panzea file gatewayIf a download link doesn't open, try right-clicking it and opening it in a new tab. Looking for other data? See Genotypes, Genome annotations and RNA-seq data.