Table 3

Repeatability measures for each duplicate pair after 3rd, 4th and 5th step of the variant validation procedure and following supertype classification
Read no Verified alleles / ST Unverified alleles / ST Repeatability
S3 S4 S5 ST S3 S4 S5 ST S3 S4 S5 ST
duplicate-1 528 - 668 31 28 28 9 120 10 0 0 0.21 0.74 1 1
duplicate-2 387 - 418 29 29 28 11 71 14 0 0 0.29 0.67 1 1
duplicate-3 322 - 501 22 22 22 13 54 6 0 0 0.29 0.79 1 1
duplicate-4 471 - 507 26 25 22 9 71 7 0 0 0.27 0.78 1 1
duplicate-5 267 - 484 21 21 21 8 40 6 0 0 0.34 0.78 1 1
duplicate-6 276 - 456 21 20 20 10 52 4 0 0 0.29 0.83 1 1
duplicate-7 288 - 319 23 23 22 10 32 4 1 0 0.42 0.85 0.96 1
duplicate-8 208 - 455 21 21 20 10 50 13 2 0 0.3 0.62 0.91 1
duplicate-9 272 - 289 27 26 23 10 34 3 3 1 0.44 0.89 0.88 0.91
duplicate-10 240 - 471 21 21 18 10 66 20 3 1 0.24 0.51 0.86 0.91
duplicate-11 230 - 236 24 24 21 11 26 6 4 1 0.48 0.8 0.84 0.92
duplicate-12 240 - 570 20 20 19 10 50 22 4 2 0.29 0.48 0.83 0.83
Average 287 - 448 24 23 22 10 56 9.6 1.4 0.4 0.32 0.73 0.94 0.96

ST – supertypes; read no - the number of reads per sample. Verified alleles/supertypes stand for the number of identical alleles/supertypes between the duplicate samples. Unverified alleles/supertypes represent the number of alleles/supertypes that were found in one of the samples and indicate non-identical genotypes. Repeatability was calculated as the ratio of verified alleles/supertypes to the total number of alleles/supertypes for each duplicate. A repeatability value of 1 signifies identical genotypes. For a duplicate each measurement was calculated four times - after the 3rd, 4th and 5th steps of the variant validation procedure, and following supertype classification. The average values for each measure are provided in the bottom row.

Sepil et al.

Sepil et al. BMC Evolutionary Biology 2012 12:68   doi:10.1186/1471-2148-12-68

Open Data