Genotyping experiment 2015GBS_MN
Description
| Experiment Short Name | MN_GBS_S15 |
| Platform | GBS restriction site |
| Data Program | USDA-ARS Fargo, ND (NDG) |
| Breeding Program | University of Minnesota - Agronomy (MN) |
| OPA Name | NA |
| Processing Date | 12/15/15 |
| Software | FastQC, Fastx Toolkit, Cutadapt, Bowtie2, SAMTools, GATK, VCFTools, same protocol at Poland et al (2012) |
| Software version | 0.11.2, 0.0.14, 1.8.1, 2.2.4, 0.1.18, 3.4-46, 0.1.14 |
| Comments | Illumina Hi-Seq 2000, VCF file filtered for: QUAL gte 40, GQ gte 40, DP gte 5, mean DP gte 10 |
235216 markers were assayed for 1498 lines.
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| Removed by filtering | Remaining |
| 191103 markers have a minor allele frequency (MAF) less than 5%
232543 markers are missing more than 10% of data 234105 markers removed | 1111 markers |
Maximum Missing Data: %
Minimum MAF: %
Additional files available
| Samples (germplasm lines) | |
| Manifest (markers used) | |
| Cluster File | |
| Raw data |