Page 44 - The prevalence of the Val66Met polymorphism in musicians: Possible evidence for compensatory neuroplasticity from a pilot study

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Table 1
(A) Accuracy statistics for each sample when compared to Genome in a Bottle (GIAB)/NIST genotypes. Two replicates of each
sample were compared. (B) Precision statistics between sample replicates.
A
Call Rate SNPs Missing SNP Rate
Sample ID Concordance at Called Sites (%) Missing SNPs
(%) Called (%)
99.30 388 0.07
NA12878 593,783 99.94
99.30 370 0.06
99.94 305 0.06
NA24385 548,279 99.93
99.94 293 0.05
99.94 260 0.05
NA24631 556,487 99.95
99.93 311 0.06

B
SNPs Concordance at Called Sites Missing SNP Rate
Sample ID Missing SNPs
Called (%) (%)
NA12878 593,783 >99.99 634 0.11
NA24385 548,279 >99.99 499 0.09
NA24631 556,487 >99.99 476 0.09

Table 2
Call rate and concordance statistics for NA12878 at each DNA input level, averaged across replicates. The total number of
SNPs genotyped is 635,930. The missing SNPs columns show the number/percent of SNPs where genotypes were missing in
either the 200 ng sample (considered the truth data for comparison) or the lower input sample, preventing a concordance
comparison across the two samples. The missing SNPs columns show the number/percent of SNPs where genotypes were
missing in either the 200 ng sample (considered the truth data for comparison) or the lower input sample, preventing a
concordance comparison across the two samples.
Discordant Concordance at Called Sites Missing Call rate
Input (ng) Concordant SNPs
SNPs (%) SNPs (%)
40 635112 2 >99.99 816 99.93
20 635065 4 >99.99 861 99.92
8 634421 26 >99.99 1484 99.82
2 633999 34 >99.99 1896 99.76
1 631370 222 99.97 4338 99.37
0.2 615564 2000 99.69 18366 97.16

Developmental Validation of the Illumina Infinium Assay using the Global Screening Array (GSA) on the iScan System for use in Forensic Laboratories