Genotyping experiment 2017_WheatCAP
Description
| Experiment Short Name | WheatCap |
| Platform | sequence capture |
| Data Program | Kansas State University - Akhunov Lab (KSA) |
| Breeding Program | Kansas State University (KSM) |
| OPA Name | none |
| Processing Date | 6/23/17 |
| Software | none |
| Software version | none |
| Comments | Genotype data from exome capture of all parents of bi-parental families being used for fine mapping of yield component QTL in the Wheat CAP project. Variant calling done using the GATK. Filtered to remove multiallelic SNPs, removed heterozygous sites, and keep only those singletons that had depth of coverage of 10x. The data will be used to determine the predicted effect of polymorphisms in the coding regions using SIFT and tools developed by T3. The data was aligned to IWGSC WGA v1.0. |
976558 markers were assayed for 36 lines.
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| Removed by filtering | Remaining |
| 136283 markers have a minor allele frequency (MAF) less than 5%
352095 markers are missing more than 10% of data 467287 markers removed | 509271 markers |
Maximum Missing Data: %
Minimum MAF: %
Additional files available
| Samples (germplasm lines) | |
| Manifest (markers used) | |
| Cluster File | |
| Raw data | all_filtered_snps_0.25_biallelic_het_SingleDp10.FullCoor.hmp |