Skip to main content

Table 4 Number of SNPs in six classes after applying reproducibility, variance and nMinorHom filters

From: Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa

SNP class No. of SNPs No. of SNPs in category
   SNP mSNP Indel SNP-SNP Indel-SNP SNP-in-Insertion F1D Codon-based
MHR 18,958 9,913 191 2,458 737 286 1,114 1,864 2,395
CRBT 5,876 4,248 0 542 761 96 144 44 41
Other 9,755 6,014 0 1,214 1,387 196 428 150 366
NMH 36,088 25,782 1,050 3,365 979 298 843 1,498 2,273
OTV 1,030 415 1 106 126 21 11 38 312
PHR 23,355 16,891 519 1,843 3,101 280 303 157 261
Reproducibility 3,263 2,568 129 200 182 17 39 55 73
AAvarianceY 491 339 10 38 82 8 8 1 5
ABvarianceX 1,775 1,095 11 221 328 32 32 18 38
ABvarianceY 3,212 2,367 54 279 384 51 34 14 29
BBvarianceY 394 183 6 43 144 7 5 2 4
nMinorHom 1,611 1,153 87 176 53 17 31 33 61
Filtered PHR 12,609 9,186 222 886 1,928 148 154 34 51
No of markers on array 95,063 63,263 1,761 9,528 7,092 1,177 2,843 3,751 5,648
  1. These SNP classes were: MHR (Mono High Resolution), which passed all QC but were monomorphic; CRBT (CallRate Below Threshold), where genotype call rate was under 97%; Other, where the resultant SNP cluster pattern did not fall into any of the other classes; NMH (No Minor Homozygote), which passed all QC but only two clusters were observed; OTV (Off-Target Variant), which had an additional low intensity cluster resulting from mismatches between the probe and the sequences for that group of individuals; and PHR (Poly High Resolution) which were polymorphic and passed all QC. PHR SNPs were subjected to additional filters (reproducibility, variance and nMinorHom).
\