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Based on genotyping of the ~400 O. sativa samples in our diversity panel, >90% of the 44,100 SNPs on the array passed our QC criteria.
A total of 5182 genes representing 74% of the genes present on the array passed through our analysis filters (see Methods).
As a consequence only 8% of the SNP on the array passed our stringent filter criteria.
Each array passed all quality control standards as recommended by the manufacturer, Agilent Technologies.
A total of 4432 genes that represented 63% of the genes present in the array passed through our stringent analysis filters.
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The remaining 10 samples that did not meet this standard however had one hybridized array passing or approaching this call rate standard (i.e., 93% of all the SNPs in the array were successfully called).
A total of 1024 study participants were successfully genotyped using the Illumina 1 M single-nucleotide polymorphism (SNP) genotyping array, passing inclusion criteria into the study.
All arrays passed quality control by DCHIP.
All arrays passed standard Affymetrix quality control: GAPDH 3'–5' ratio 1.07±0.005, RawQ 2.73±0.02, Background noise 79.3±0.6.
All 90 samples hybridized on the arrays passed the p95 and average signal quality control (see methods for details).
All RMA-normalized arrays passed the statistical quality control provided by the function arrayQualityMetrics in the R-package arrayQualityMetrics [23].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com