Table 2. Genes showing evidence of genotype-dependent allelic imbalance in SAM/ORE “hybrid” wild-type and sdE3 mutant flies.
| Gene | ORE count (mut. 1) | SAM count (mut. 1) | ORE count (mut. 2) | SAM count (mut. 2) | ORE count (WT 1) | SAM count (WT 1) | ORE count (WT 2) | SAM count (WT 2) | P | q |
|---|---|---|---|---|---|---|---|---|---|---|
| CG6308 | 0 | 115 | 0 | 109 | 96 | 0 | 0 | 0 | 5.13E-87 | 6.50E-84 |
| Reg-2 | 92 | 2 | 69 | 5 | 33 | 36 | 52 | 34 | 7.51E-20 | 4.76E-17 |
| CG12708 | 2 | 117 | 0 | 0 | 38 | 31 | 0 | 0 | 5.17E-19 | 2.18E-16 |
| CG3632 | 1 | 41 | 0 | 55 | 26 | 31 | 30 | 28 | 2.39E-18 | 7.57E-16 |
| CG6739 | 7 | 1 | 9 | 2 | 0 | 17 | 0 | 21 | 8.79E-13 | 2.23E-10 |
| mthl10 | 8 | 0 | 9 | 0 | 0 | 5 | 0 | 6 | 9.05E-10 | 1.91E-07 |
| mtm | 9 | 0 | 5 | 0 | 0 | 7 | 0 | 5 | 2.09E-09 | 3.78E-07 |
| CG4452 | 14 | 8 | 5 | 12 | 22 | 0 | 17 | 0 | 3.72E-09 | 5.89E-07 |
| CG33785 | 2 | 5 | 5 | 7 | 19 | 0 | 15 | 0 | 1.81E-08 | 2.52E-06 |
| CG6310 | 75 | 82 | 85 | 75 | 50 | 102 | 30 | 102 | 1.99E-08 | 2.52E-06 |
| CG2147 | 13 | 0 | 19 | 0 | 26 | 0 | 0 | 25 | 2.73E-08 | 3.14E-06 |
| CG9281 | 0 | 14 | 0 | 17 | 7 | 9 | 8 | 3 | 6.49E-08 | 6.85E-06 |
| CG1908 | 16 | 3 | 16 | 4 | 4 | 27 | 11 | 12 | 9.89E-08 | 9.64E-06 |
| Spt5 | 93 | 45 | 74 | 55 | 81 | 105 | 73 | 111 | 1.66E-07 | 1.45E-05 |
| mth | 65 | 13 | 0 | 0 | 49 | 57 | 63 | 51 | 1.72E-07 | 1.45E-05 |
| CG1140 | 30 | 6 | 21 | 5 | 8 | 13 | 10 | 20 | 2.16E-07 | 1.71E-05 |
| CG1542 | 10 | 14 | 14 | 15 | 33 | 3 | 22 | 4 | 3.03E-07 | 2.26E-05 |
| CG6051 | 15 | 2 | 8 | 3 | 5 | 25 | 11 | 17 | 1.03E-06 | 6.89E-05 |
| U3-55K | 0 | 0 | 32 | 62 | 42 | 22 | 34 | 14 | 1.03E-06 | 6.89E-05 |
| CG5704 | 4 | 0 | 2 | 0 | 0 | 7 | 0 | 6 | 1.13E-06 | 7.14E-05 |
| CG32202 | 1 | 8 | 0 | 9 | 12 | 1 | 11 | 9 | 2.31E-06 | 1.39E-04 |
| CG5626 | 1 | 19 | 1 | 18 | 9 | 12 | 11 | 8 | 2.42E-06 | 1.39E-04 |
| CG16888 | 0 | 2 | 0 | 3 | 7 | 0 | 7 | 0 | 2.87E-06 | 1.58E-04 |
| scaf6 | 0 | 3 | 0 | 3 | 3 | 0 | 7 | 0 | 4.20E-06 | 2.22E-04 |
| CG16799 | 0 | 18 | 0 | 12 | 7 | 8 | 5 | 9 | 6.75E-06 | 3.42E-04 |
| RpL7-like | 0 | 0 | 345 | 239 | 0 | 0 | 279 | 325 | 8.50E-06 | 4.14E-04 |
| CAH2 | 4 | 10 | 0 | 0 | 13 | 0 | 8 | 1 | 1.04E-05 | 4.90E-04 |
| CG4908 | 21 | 6 | 15 | 10 | 5 | 19 | 6 | 13 | 1.62E-05 | 7.33E-04 |
| CG1673 | 0 | 2 | 0 | 5 | 2 | 0 | 4 | 0 | 2.27E-05 | 9.94E-04 |
| CG2260 | 0 | 0 | 120 | 34 | 122 | 69 | 106 | 88 | 2.63E-05 | 1.09E-03 |
| Chc | 4 | 0 | 7 | 0 | 10 | 13 | 2 | 8 | 2.66E-05 | 1.09E-03 |
| RpL7-like | 5 | 1 | 5 | 3 | 0 | 7 | 2 | 16 | 2.94E-05 | 1.16E-03 |
| CG30286 | 0 | 6 | 0 | 5 | 2 | 0 | 2 | 0 | 3.03E-05 | 1.16E-03 |
| CG9005 | 0 | 3 | 0 | 5 | 0 | 0 | 5 | 0 | 3.15E-05 | 1.17E-03 |
| Pep | 1 | 3 | 3 | 8 | 10 | 0 | 0 | 0 | 3.94E-05 | 1.43E-03 |
| CG12424 | 3 | 0 | 5 | 1 | 2 | 22 | 5 | 10 | 4.53E-05 | 1.51E-03 |
| Khc-73 | 2 | 0 | 4 | 0 | 0 | 3 | 0 | 3 | 4.53E-05 | 1.51E-03 |
| CG13749 | 0 | 3 | 0 | 3 | 4 | 0 | 2 | 0 | 4.53E-05 | 1.51E-03 |
| CG12009 | 2 | 2 | 2 | 4 | 8 | 0 | 12 | 0 | 4.70E-05 | 1.53E-03 |
| D12 | 15 | 5 | 0 | 0 | 5 | 19 | 5 | 16 | 5.00E-05 | 1.56E-03 |
| Aats-glupro | 8 | 1 | 4 | 0 | 1 | 3 | 1 | 7 | 5.04E-05 | 1.56E-03 |
| CG5144 | 3 | 0 | 2 | 0 | 0 | 2 | 0 | 5 | 5.40E-05 | 1.62E-03 |
| Lap1 | 3 | 4 | 10 | 4 | 34 | 2 | 30 | 0 | 5.59E-05 | 1.62E-03 |
| CG17841 | 24 | 4 | 17 | 3 | 15 | 19 | 21 | 16 | 5.61E-05 | 1.62E-03 |
| Eip71CD | 0 | 0 | 9 | 0 | 0 | 0 | 0 | 4 | 6.17E-05 | 1.70E-03 |
| CG7376 | 0 | 0 | 0 | 4 | 5 | 0 | 4 | 0 | 6.17E-05 | 1.70E-03 |
| CG10650 | 4 | 1 | 4 | 0 | 0 | 5 | 0 | 2 | 6.67E-05 | 1.70E-03 |
| CG15382 | 1 | 1 | 6 | 0 | 0 | 5 | 0 | 3 | 6.67E-05 | 1.70E-03 |
| Not1 | 4 | 1 | 3 | 0 | 0 | 6 | 0 | 2 | 6.67E-05 | 1.70E-03 |
| CG5189 | 6 | 1 | 6 | 0 | 0 | 1 | 0 | 4 | 6.81E-05 | 1.70E-03 |
P-values are derived from likelihood ratio tests comparing a model with genotype-dependent allelic imbalance to a model with the same level of allelic imbalance in wild-type and sdE3 flies, and q-values were generated using the qvalue package in R. Top 50 genes are shown.