Table 2. Peak Location and LOD Score of Each QTL Depicted in Figure 1.
| Name | Trait | Trait_Type | Chr | Peak (cM) | Peak (Mb) | LOD | FDR* | Period |
| Q1@39 | Onset REM | Fragmentation | 1 | 38.470 | 109.044 | 4.445 | .006 | 24 hour |
| Q1@39 | db TS | Fragmentation | 1 | 39.120 | 115.677 | 3.453 | .034 | 24 hour |
| Q1@39 | db NREM | Fragmentation | 1 | 39.120 | 115.677 | 3.438 | .034 | 24 hour |
| Q1@39 | nb NREM | Fragmentation | 1 | 42.400 | 133.902 | 3.485 | .026 | 24 hour |
| Q1@39 | # Shifts | Fragmentation | 1 | 42.400 | 133.902 | 3.076 | .033 | 24 hour |
| Q1@64 | # Arousals | Fragmentation | 1 | 62.230 | 172.886 | 4.231 | .004 | 24 hour |
| Q1@64 | lat REM | Latency | 1 | 62.230 | 172.886 | 2.941 | .046 | 24 hour |
| Q1@64 | db Wake | Fragmentation | 1 | 62.230 | 172.886 | 3.991 | .019 | Dark |
| Q1@64 | nb Wake | Fragmentation | 1 | 63.680 | 176.451 | 3.285 | .018 | Dark |
| Q1@64 | REM rel Theta I | Power Bands | 1 | 63.680 | 176.451 | 2.790 | .040 | Mixed |
| Q1@75 | lat NREM | Latency | 1 | 74.200 | 187.588 | 4.528 | .001 | 24 hour |
| Q1@75 | db TS | Fragmentation | 1 | 74.200 | 187.588 | 3.252 | .023 | Dark |
| Q1@75 | lat NREM | Latency | 1 | 74.200 | 187.588 | 2.796 | .019 | Dark |
| Q1@75 | NREM rel Delta | Power Bands | 1 | 74.200 | 187.588 | 3.097 | .044 | Mixed |
| Q1@75 | Onset REM | Fragmentation | 1 | 74.580 | 188.870 | 3.475 | .009 | Dark |
| Q1@75 | db NREM | Fragmentation | 1 | 76.960 | 189.312 | 3.176 | .027 | Dark |
| Q1@75 | # Arousals | Fragmentation | 1 | 76.960 | 189.312 | 2.493 | .041 | Dark |
| Q3@12 | NREM rel Delta | Power Bands | 3 | 12.180 | 30.690 | 2.745 | .042 | Mixed |
| Q3@71 | lat NREM | Latency | 3 | 71.060 | 146.067 | 3.244 | .027 | 24 hour |
| Q5@49 | % REM/TS | REM | 5 | 45.290 | 65.322 | 4.225 | .008 | 24 hour |
| Q5@49 | db REM | REM | 5 | 49.320 | 70.388 | 6.339 | .001 | 24 hour |
| Q5@49 | REM | REM | 5 | 51.940 | 73.499 | 4.224 | .005 | 24 hour |
| Q6@70 | # Shifts | Fragmentation | 6 | 70.000 | 135.767 | 3.111 | .040 | 24 hour |
| Q6@70 | nb NREM | Fragmentation | 6 | 70.000 | 135.767 | 3.079 | .033 | 24 hour |
| Q6@70 | db Wake | Fragmentation | 6 | 70.000 | 135.767 | 3.666 | .024 | 24 hour |
| Q7@1 | db Wake | Fragmentation | 7 | 0.980 | 7.882 | 3.113 | .045 | 24 hour |
| Q7@1 | nb Wake | Fragmentation | 7 | 0.980 | 7.882 | 4.064 | .012 | 24 hour |
| Q7@32 | nb REM | REM | 7 | 31.770 | 50.217 | 4.288 | .002 | Mixed |
| Q7@40 | REM min | REM | 7 | 40.200 | 67.412 | 3.608 | .004 | Light |
| Q7@63 | Inter REM | REM | 7 | 59.900 | 102.969 | 4.014 | .046 | Mixed |
| Q7@63 | Wake min | State Length | 7 | 62.850 | 114.066 | 4.812 | .022 | Mixed |
| Q7@63 | NREM min | State Length | 7 | 65.140 | 114.924 | 4.443 | .027 | Light |
| Q9@15 | lat NREM | Latency | 9 | 15.160 | 46.527 | 3.062 | .026 | 24 hour |
| Q12@28 | db TS | Fragmentation | 12 | 27.580 | 71.050 | 3.111 | .035 | 24 hour |
| Q12@28 | db NREM | Fragmentation | 12 | 27.580 | 71.050 | 3.119 | .036 | 24 hour |
| Q13@2 | # Arousals | Fragmentation | 13 | 0.000 | 4.692 | 2.536 | .049 | Light |
| Q13@2 | lat REM | Latency | 13 | 1.640 | 14.548 | 2.829 | .042 | 24 hour |
| Q13@2 | Wake min | State Length | 13 | 1.970 | 16.724 | 5.139 | .001 | 24 hour |
| Q13@2 | NREM min | State Length | 13 | 1.970 | 16.724 | 3.593 | .049 | 24 hour |
| Q13@23 | db REM | REM | 13 | 20.030 | 60.142 | 3.299 | .026 | 24 hour |
| Q13@23 | REM min | REM | 13 | 22.660 | 68.690 | 6.302 | <.001 | 24 hour |
| Q13@23 | % REM/TS | REM | 13 | 22.660 | 68.690 | 6.473 | <.001 | 24 hour |
| Q13@23 | Inter REM | REM | 13 | 25.940 | 72.819 | 3.928 | .012 | 24 hour |
| Q14@73 | lat REM | Latency | 14 | 72.980 | 121.782 | 3.058 | .046 | 24 hour |
| Q15@26 | % REM/TS | REM | 15 | 26.300 | 82.415 | 4.040 | .002 | Dark |
| Q16@24 | REM rel Theta I | Power Bands | 16 | 23.660 | 51.539 | 3.039 | .037 | Mixed |
| Q17@13 | % REM/TS | REM | 17 | 3.940 | 24.849 | 4.263 | .002 | Mixed |
| Q17@13 | db TS | Fragmentation | 17 | 13.120 | 44.789 | 2.601 | .049 | Mixed |
| Q17@29 | nb REM | REM | 17 | 28.590 | 65.200 | 3.021 | .014 | Mixed |
| Q17@29 | REM min | REM | 17 | 28.590 | 65.200 | 4.870 | <.001 | Mixed |
| Q17@29 | Wake min | State Length | 17 | 30.230 | 65.622 | 7.562 | <.001 | Mixed |
| Q17@29 | NREM min | State Length | 17 | 30.230 | 65.622 | 5.954 | .001 | Dark |
QTL were detected by R package QTL as were the peak LOD scores. The QTL peak was defined as the position within the QTL with the highest LOD score. Trait type was determined by factor analysis (Table 1). Chr = chromosome, LOD = logarithm of odds. FDR = False Discovery Rate (probability). See Supplementary Information for complete trait descriptions. See Supporting Information Table S3 for further information about each QTL.
To account for multiple testing using a non-parametric approach, FDR estimates were computed genome-wide within each sleep trait by permuting individual identifiers for the genotype data and repeating the analyses on 1000 replicate permuted data sets [25]. To eliminate the influence of markers in high linkage disequilibrium, chromosome-wide peak marker LOD scores were used for all FDR computations.