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SNPs were excluded with call rate <95%, MAF <0.05, Hardy-Weinberg Equilibrium (HWE) p-value < 10-4, or unresolved replicate errors, and samples were excluded with call rate <95%, ambiguous gender, or predicted less than 80% European ancestry.
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Statistical analysis shows that the difference between slopes is significant within the dataset but that the deviation is within that assessed previously for replicate error using DLS to describe particle systems changing in time.
The OOB replicate error rate estimate is always computed.
GeneSpring's replicate error model was used for our analysis.
For the SNPs genotyped, all genotypes between duplicates were consistent (0% replicate error rate).
Replicate error analysis was performed to verify the relationships among the samples (Table S1).
For the SNP genotyping, we performed data cleaning, filtering, SNP calling, and replicate error analysis with GenomeStudio.
Replicate error analysis was performed in GenomeStudio and refers to the fraction of genotypes that are identical for each pair of samples tested.
For quality comparison purposes, we genotyped a subset of the sample in duplicate in order to estimate the replicate error rate.
All genotype experiments were made at least in duplicate, with quality control of automated allele calling by two independent operators blind to phenotype (0% replicate error rate).
Precision describes how accurately the hybridization signal intensity can be reproduced and is usually reported as a correlation coefficient, standard deviation or average replicate error between duplicated experiments using the same RNA sample [ 19].
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