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Table 2 Allelic imbalance detection accuracy in alignments using partial or no genotypes compared to complete genotypes

From: Removing reference mapping biases using limited or no genotype data identifies allelic differences in protein binding at disease-associated loci

Factor/Assay (Condition) Completea Partial Genotypeb Imbalances No Genotypec Imbalances
Total Partial None Total Known variants Predicted variants Total Known variants Predicted variants
Nt Nimp Ncom Nt Sens Prec Nimp Sens Prec Nt-Nimp Sens Prec Nt Sens Prec Ncom Sens Prec Nt-Ncom Sens Prec
CREB1 (50 bp) 200 125 141 190 73.0 76.8 134 96.8 90.3 56 33.3 44.6 203 76.0 74.9 160 93.6 82.5 43 33.9 46.5
CREB1 (35 bp) 106 70 81 104 73.6 75.0 74 97.1 91.9 30 27.8 33.3 107 77.4 76.6 87 92.6 86.2 20 28.0 35.0
CREB1 (20 bp) 26 16 16 24 69.2 75.0 17 100.0 94.1 7 20.0 28.6 22 69.2 81.8 17 100.0 94.1 5 20.0 40.0
CTCF (35 bp) 267 187 192 300 83.1 74.0 198 98.4 92.9 102 47.5 37.3 298 85.0 76.2 210 97.9 89.5 88 52.0 44.3
DNase (20 bp) 104 43 47 138 51.0 38.4 42 97.7 100.0 96 18.0 11.5 144 51.9 37.5 55 97.9 83.6 89 14.0 9.0
CREB1 (2 alns)d 200 125 141 195 78.5 80.5 135 97.6 90.4 60 46.7 58.3 204 77.0 75.5 156 92.2 83.3 48 40.7 50.0
Mismatches alllowed                     
CREB1 (0 mm) 199 122 138 137 58.8 85.4 137 95.9 85.4 0 - - 160 63.3 78.8 160 91.3 78.8 0 - -
CREB1 (1 m m)e 200 125 141 190 73.0 76.8 134 96.8 90.3 56 33.3 44.6 203 76.0 74.9 160 93.6 82.5 43 33.9 46.5
CREB1 (2 mm) 199 124 137 245 80.4 65.3 133 97.6 91.0 112 52.0 34.8 251 81.4 64.5 159 96.4 83.0 92 48.4 32.6
CREB1 (3 mm) 213 123 143 301 79.2 53.2 132 98.4 90.9 169 50.0 23.7 313 81.7 52.7 161 96.4 83.9 152 47.6 19.7
Minimum reads/allele                     
CREB1 (2 reads) 301 178 199 486 73.4 45.5 187 97.2 92.5 299 39.0 16.1 515 75.4 44.1 228 95.0 82.9 287 37.3 13.2
CREB1 (3 reads) 261 156 173 267 70.1 68.8 162 94.9 91.4 105 33.3 33.3 289 72.8 65.7 191 92.5 83.8 98 34.1 30.6
CREB1 (4 reads) 230 142 159 218 71.4 76.0 148 95.1 91.2 70 33.7 42.6 235 74.8 73.2 175 92.5 84.0 60 35.2 41.7
CREB1 (5 reads)e 200 125 141 190 73.0 76.8 134 96.8 90.3 56 33.3 44.6 203 76.0 74.9 160 93.6 82.5 43 33.9 46.5
CREB1 (6 reads) 198 122 136 174 70.7 80.5 130 96.7 90.8 44 28.9 50.0 188 73.7 77.7 153 93.4 83.0 35 30.6 54.3
CREB1 (7 reads) 173 109 123 154 72.8 81.8 116 97.2 91.4 38 31.2 52.6 167 75.7 78.4 138 92.7 82.6 29 34.0 58.6
CREB1 (8 reads) 157 100 111 141 72.0 80.1 107 97.0 90.7 34 28.1 47.1 148 75.2 79.7 124 92.8 83.1 24 32.6 62.5
CREB1 (9 reads) 144 91 101 130 72.2 80.0 98 96.7 89.8 32 30.2 50.0 140 75.7 77.9 115 93.1 81.7 25 34.9 60.0
CREB1 (10 reads) 124 80 88 117 74.2 78.6 88 96.2 87.5 29 34.1 51.7 125 76.6 76.0 102 92.0 79.4 23 38.9 60.9
CREB1 (15 reads) 88 60 66 82 77.3 82.9 66 96.7 87.9 16 35.7 62.5 88 80.7 80.7 76 92.4 80.3 12 45.5 83.3
CREB1 (20 reads) 63 47 52 64 84.1 82.8 53 97.9 86.8 11 43.8 63.6 67 88.9 83.6 60 96.2 83.3 7 54.5 85.7
Imputation Rsq threshold                     
CREB1 (Rsq > .3) e 200 125 - 190 73.0 76.8 134 96.8 90.3 56 33.3 44.6 - - - - - - - - -
CREB1 (Rsq > .4) 200 122 - 190 72.5 76.3 133 97.5 89.5 57 33.3 45.6 - - - - - - - - -
CREB1 (Rsq > .5) 200 121 - 187 72.5 77.5 129 98.3 92.2 58 32.9 44.8 - - - - - - - - -
CREB1 (Rsq > .6) 200 118 - 186 72.5 78.0 124 98.3 93.5 62 35.4 46.8 - - - - - - - - -
CREB1 (Rsq > .7) 200 117 - 185 72.0 77.8 123 98.3 93.5 62 34.9 46.8 - - - - - - - - -
CREB1 (Rsq > .8) 200 104 - 182 70.5 77.5 111 99.0 92.8 71 39.6 53.5 - - - - - - - - -
CREB1 (Rsq > .9) 200 96 - 176 69.5 79.0 99 99.0 96.0 77 42.3 57.1 - - - - - - - - -
  1. aComplete genotype alignments use sequencing-based genotypes bPartial genotype alignments use array-based genotypes and imputation cNo genotypes alignments use common variants (MAF > .05) from 1000 Genomes EUR dImbalances called after a second alignment using refined genotypes; known variants are variants included in the first alignment eCondition used by default by AA-ALIGNER; Nt total imbalance count, Nimp imbalances at heterozygous sites identified by imputation, Ncom imbalances at common variants, Sens, percent sensitivity, Prec, percent precision