Table 4 Genotype comparison
| Â | Â | Â | RNASeq | RNASeq | BeadXPress | Â | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Â | Â | Â | Genotypes | SNP quality score | Genotypes | Â | ||||||
SNP | SNP ID1 | SNP name | LIM1 | LIM2 | LIM3 | LIM1 | LIM2 | LIM3 | LIM1 | LIM2 | LIM3 | Concordance (%) |
1 | rs43270801 | 1_127257294 | TT | TT | TT | 35 | 35 | 38 | -- | -- | -- | Â |
3 | rs43299525 | 2_29938364 | TT | TC | TC | 4 | 4 | 3 | TT | TC | TT | 66.67 |
4 | rs42982977 | 3_54421677 | AG | GG | AG | 46 | 13 | 14 | -- | -- | -- | Â |
5 | rs41255286 | 3_90246130 | CC | CC | CT | 99 | 99 | 99 | CC | CC | CT | 100.00 |
6 | rs43360668 | 3_100666640 | CC | CC | CC | 14 | 9 | 6 | CC | CC | CC | 100.00 |
7 | rs43414903 | 4_115404252 | CC | CT | CC | 71 | 99 | 92 | CC | CT | CC | 100.00 |
9 | rs43484023 | 6_109946655 | GG | GC | GG | 5 | 5 | 5 | GC | GG | CC | 33.33 |
11 | rs42722878 | 8_101639394 | TC | CC | TT | 3 | 3 | 4 | TT | TC | TC | 0.00 |
12 | rs42722887 | 8_101642585 | AA | GA | GA | 14 | 26 | 3 | AA | GA | GA | 100.00 |
13 | rs42722900 | 8_101645192 | CC | CC | CT | 8 | 4 | 55 | CC | CC | CT | 100.00 |
14 | rs42722901 | 8_101645255 | TT | CT | CT | 6 | 15 | 4 | TT | CT | CT | 100.00 |
15 | rs42306198 | 8_111749876 | GG | GG | GA | 79 | 82 | 99 | GG | GG | GA | 100.00 |
16 | rs17870317 | 9_34687597 | TG | TG | TG | 3 | 3 | 3 | TT | TT | TG | 33.33 |
17 | rs17870361 | 9_61258934 | CT | CC | CT | 54 | 20 | 21 | CT | CC | CT | 100.00 |
18 | rs43626955 | 10_51842959 | CC | CC | CC | 99 | 99 | 99 | CC | CC | CC | 100.00 |
19 | rs43626956 | 10_51843008 | GG | GG | GG | 99 | 99 | 99 | GG | GG | GG | 100.00 |
20 | rs43626957 | 10_51843101 | GG | GG | GG | 79 | 76 | 76 | GG | GG | GG | 100.00 |
21 | rs42284472 | 10_58147435 | CC | CT | CC | 14 | 11 | 8 | -- | -- | -- | Â |
22 | rs42748012 | 10_90111114 | CT | CT | CC | 19 | 59 | 65 | CT | CT | CC | 100.00 |
23 | rs42738663 | 10_90126463 | AG | AA | GG | 72 | 16 | 23 | AG | AG | GG | 66.67 |
24 | rs42311164 | 11_47748651 | GC | CC | GC | 29 | 24 | 77 | GC | GG | GC | 100.00 |
25 | rs42613762 | 13_51391698 | AA | AA | GG | 4 | 8 | 6 | AA | AA | GG | 100.00 |
26 | rs42555633 | 13_59146558 | AG | AA | AG | 3 | 4 | 49 | AG | AG | AA | 33.33 |
27 | rs41255356 | 13_67838559 | CC | TC | CC | 4 | 6 | 4 | TC | TT | CC | 33.33 |
28 | rs41712055 | 13_78093743 | CT | TT | CC | 30 | 21 | 24 | TT | TT | -- | Â |
29 | rs42929124 | 15_17647017 | AA | AA | AA | 23 | 20 | 23 | -- | -- | -- | Â |
30 | rs41774805 | 15_57309934 | AA | GA | GA | 8 | 47 | 68 | AA | GA | GA | 100.00 |
31 | rs41720009 | 17_68389438 | GG | GG | GG | 31 | 43 | 34 | AG | GG | GG | 66.67 |
32 | rs41905209 | 19_25255424 | CT | CC | CC | 22 | 10 | 54 | CT | CT | CC | 66.67 |
33 | rs42803062 | 19_28474511 | CC | CT | CT | 52 | 33 | 62 | CC | CT | CT | 100.00 |
34 | rs41930998 | 19_62070112 | CC | CT | CT | 14 | 6 | 4 | -- | -- | -- | Â |
35 | rs41969933 | 21_19283173 | TT | CT | TT | 5 | 5 | 5 | TT | CT | TT | 100.00 |
36 | rs42013154 | 22_48725986 | GT | GT | GG | 99 | 99 | 99 | GT | GT | GG | 100.00 |
37 | rs42016156 | 22_49203698 | TT | TT | CC | 48 | 24 | 27 | TT | TT | CC | 100.00 |
38 | rs42015934 | 22_51561550 | CC | CT | CC | 29 | 6 | 35 | CC | CT | CC | 100.00 |
39 | rs42451508 | 25_21535844 | GA | GA | GA | 39 | 31 | 70 | GA | GA | GA | 100.00 |
40 | rs42174698 | 29_26367840 | CC | CC | CC | 52 | 40 | 70 | CC | CC | CC | 100.00 |
41 | rs17871172 | 29_26368230 | CC | CC | CT | 56 | 47 | 30 | CC | CC | CT | 100.00 |
42 | rs17871173 | 29_26368263 | CT | TT | CT | 99 | 37 | 99 | -- | -- | -- | Â |
43 | rs42188815 | 29_41795763 | AA | AA | AA | 99 | 99 | 99 | -- | -- | -- | Â |
44 | rs42188070 | 29_45033799 | CC | CT | CC | 26 | 26 | 14 | CC | CT | CC | 100.00 |
45 | rs29024659 | X_81605181 | TT | TT | TT | 26 | 26 | 29 | TT | TT | TT | 100.00 |
46 | rs55617351 | X_141005664 | GA | GA | GA | 3 | 3 | 3 | GG | GG | GG | 0.00 |
47 | rs55617145 | X_141005870 | CA | CA | CA | 3 | 3 | 3 | CC | CC | CC | 0.00 |
48 | rs55617174 | X_141005964 | AT | AT | AT | 3 | 3 | 3 | TT | TT | TT | 0.00 |