Table 2. Genome-to-genome analysis results per genotype.
The table shows significant p-values (<4.7×10−6), NA representing non-significant associations. We also give odds ratio (OR) and 97% confidence interval for each significant association.
| HCV gene | Position (amino acid) |
Genotype 1a N = 3548 |
Genotype 1b N = 1924 |
Genotype 2a N = 304 |
Genotype 2b N = 472 |
Genotype 3a N = 1839 |
Genotype 4a N = 193 |
|---|---|---|---|---|---|---|---|
| NS3 | 1332(A) | 1.02e-10 (OR 1.06; 1.04–1.08) |
NA | NA | NA | NA | NA |
| NS3 | 1355(I) | 3.14e-07 (OR 1.1; 1.06–1.14) |
NA | NA | NA | NA | NA |
| NS3 | 1370(I) | NA | 1.09e-08 (OR 0.83; 0.78–0.88) |
NA | NA | NA | NA |
| NS3 | 1370(T) | NA | 4.87e-08 (OR 1.2; 1.12–1.28) |
NA | NA | NA | NA |
| NS3 | 1473(D) | 3.82e-07 (OR 1.03 1.02–1.04) |
NA | NA | NA | NA | NA |
| NS3 | 1516(I) | 3.51e-07 (OR 1.06; 1.04–1.09) |
NA | NA | NA | NA | NA |
| NS3 | 1598(R) | 2.26e-07 (OR 1.04; 1.02–1.05) |
NA | NA | NA | NA | NA |
| NS3 | 1612(I) | 7.88e-16 (OR 0.86; 0.83–0.89) |
NA | NA | NA | NA | NA |
| NS3 | 1612(N) | 1.54e-11 (OR 1.09; 1.06–1.11) |
NA | NA | NA | NA | NA |
| NS3 | 1612(T) | 1.54e-08 (OR 1.11; 1.07–1.15) |
NA | NA | NA | NA | NA |
| NS3 | 1635(I) | 7e-07 (OR 1.1; 1.06–1.14) |
NA | NA | NA | NA | NA |
| NS4A | 1671(T) | 1.83e-07 (OR 1.03; 1.02–1.04) |
NA | NA | NA | NA | NA |
| NS4A | 1703(R) | NA | 6.94e-07 (OR 1.19; 1.11–1.27) |
NA | NA | NA | NA |
| NS5A | 1996(R) | 7.87e-07 (OR 1.01; 1.01–1.02) |
NA | NA | NA | NA | NA |
| NS5A | 2009(F) | NA | 1.04e-08 (OR 1.11; 1.07–1.15) |
NA | NA | NA | NA |
| NS5A | 2009(I) | 2.01e-06 (OR 1.02; 1.01–1.02) |
NA | NA | NA | NA | NA |
| NS5A | 2024(V) | 5.81e-09 (OR 1.04; 1.03–1.05) |
NA | NA | NA | NA | NA |
| NS5A | 2034(D) | 1.75e-07 (OR 1.03; 1.02–1.04) |
NA | NA | NA | NA | NA |
| NS5A | 2034(T) | NA | NA | NA | NA | 1.61e-07 (OR 0.91; 0.87–0.94) |
NA |
| NS5A | 2040(K) | 3.05e-06 (OR 0.98; 0.97–0.99) |
NA | NA | NA | NA | NA |
| NS5A | 2040(R) | 2.54e-07 (OR 1.03; 1.02–1.04) |
NA | NA | NA | NA | NA |
| NS5A | 2047(A) | 9.8e-20 (OR 1.07; 1.06–1.09) |
NA | NA | NA | NA | NA |
| NS5A | 2065(H) | 9.81e-07 (OR 1.01; 1.01–1.02) |
1.38e-07 (OR 1.06; 1.04–1.09) |
NA | NA | NA | NA |
| NS5A | 2080(K) | NA | 2.9e-18 (OR 1.12; 1.09–1.14) |
NA | NA | NA | NA |
| NS5A | 2080(R) | NA | 1.39e-06 (OR 0.95; 0.93–0.97) |
NA | NA | NA | NA |
| NS5A | 2187(R) | NA | 1.07e-06 (OR 1.07; 1.04–1.09) |
NA | NA | NA | NA |
| NS5A | 2211(L) | 2.84e-06 (OR 0.99; 0.98–0.99) |
NA | NA | NA | NA | NA |
| NS5A | 2220(R) | NA | 2.65e-06 (OR 1.03; 1.02–1.04) |
NA | NA | NA | NA |
| NS5A | 2224(L) | NA | 1.6e-12 (OR 1.05; 1.04–1.07) |
NA | NA | NA | NA |
| NS5A | 2234(W) | NA | 1.46e-07 (OR 1.06; 1.03–1.08) |
NA | NA | NA | NA |
| NS5A | 2237(K) | NA | 2.6e-12 (OR 1.06; 1.04–1.08) |
NA | NA | NA | NA |
| NS5A | 2251(I) | NA | 2.05e-11 (OR 1.07; 1.05–1.09) |
NA | NA | NA | NA |
| NS5A | 2252(I) | 1.29e-25 (OR 1.12; 1.1–1.15) |
NA | NA | NA | 8.68e-07 (OR 1.05; 1.03–1.07) |
NA |
| NS5A | 2252(V) | 1.72e-22 (OR 0.89; 0.87–0.91) |
NA | NA | NA | 5.5e-07 (OR 0.95; 0.92–0.97) |
NA |
| NS5A | 2287(I) | 1.54e-14 (OR 1.09; 1.07–1.12) |
6.24e-07 (OR 1.08; 1.05–1.11) |
NA | NA | NA | NA |
| NS5A | 2287(V) | 1.82e-10 (OR 0.92; 0.90–0.95) |
NA | NA | NA | NA | NA |
| NS5A | 2298(I) | 1.56e-06 (OR 1.05; 1.03–1.08) |
NA | NA | NA | NA | NA |
| NS5A | 2298(V) | 1.66e-14 (OR 0.92; 0.90–0.94) |
NA | NA | NA | NA | NA |
| NS5A | 2300(P) | NA | 2.7e-15 (OR 1.12; 1.09–1.15) |
NA | NA | NA | NA |
| NS5A | 2300(S) | NA | 9.41e-08 (OR 0.94; 0.91–0.96) |
NA | NA | NA | NA |
| NS5A | 2320(Q) | 5.01e-09 (OR 1.08; 1.05–1.11) |
NA | NA | NA | NA | NA |
| NS5A | 2330(R) | NA | 1.26e-06 (OR 1.03; 1.02–1.04) |
NA | NA | NA | NA |
| NS5A | 2360(A) | NA | 1.46e-12 (OR 1.12; 1.09–1.16) |
NA | NA | NA | NA |
| NS5A | 2371(S) | 2.03e-07 (OR 1.03; 1.02–1.04) |
NA | NA | NA | NA | NA |
| NS5A | 2372(A) | 2.44e-06 (OR 0.96; 0.94–0.97) |
NA | NA | NA | NA | NA |
| NS5A | 2372(S) | 1.63e-14 (OR 1.06; 1.04–1.07) |
NA | NA | NA | NA | NA |
| NS5A | 2385(C) | 3.24e-14 (OR 1.09; 1.07–1.11) |
4.35e-07 (OR 1.04; 1.03–1.06) |
NA | NA | NA | NA |
| NS5A | 2385(Y) | 2.7e-13 (OR 0.93; 0.91–0.94) |
NA | NA | NA | NA | NA |
| NS5A | 2411(G) | NA | 4.61e-08 (OR 1.11; 1.07–1.15) |
NA | NA | NA | NA |
| NS5A | 2411(S) | NA | 9.02e-07 (OR 0.92; 0.89–0.95) |
NA | NA | NA | NA |
| NS5A | 2412(K) | 5.74e-09 (OR 1.03; 1.02–1.05) |
NA | NA | NA | NA | NA |
| NS5A | 2412(T) | 7.87e-10 (OR 0.93; 0.91–0.95) |
NA | NA | NA | NA | NA |
| NS5A | 2414(D) | 2.43e-07 (OR 0.97; 0.96–0.98) |
NA | NA | NA | NA | NA |
| NS5A | 2416(G) | NA | NA | NA | NA | 5.21e-07 (OR 1.06; 1.04–1.09) |
NA |
| NS5A | 2416(N) | NA | NA | NA | NA | 2.5e-07 (OR 1.09; 1.05–1.12) |
NA |
| NS5A | 2416(S) | NA | NA | NA | NA | 1.04e-11 (OR 0.89; 0.86–0.92) |
NA |
| NS5A | 2420(N) | NA | NA | NA | NA | 3.39e-09 (OR 1.08; 1.05–1.11) |
NA |
| NS5A | 2420(S) | NA | NA | NA | NA | 7.1e-07 (OR 0.95; 0.93–0.97) |
NA |
| NS5B | 2510(N) | 2.25e-06 (OR 1.02; 1.01–1.03) |
NA | NA | NA | NA | NA |
| NS5B | 2567(I) | 1.73e-13 (OR 1.02; 1.02–1.03) |
5.73e-08 (OR 1.07; 1.04–1.09) |
NA | NA | NA | NA |
| NS5B | 2570(A) | NA | NA | NA | NA | 2.63e-07 (OR 1.11; 1.06–1.15) |
NA |
| NS5B | 2570(T) | NA | NA | NA | NA | 8.87e-15 (OR 1.11; 1.08–1.14) |
NA |
| NS5B | 2570(V) | NA | NA | NA | NA | 5.57e-20 (OR 0.84; 0.81–0.87) |
NA |
| NS5B | 2576(A) | 1.21e-11 (OR 1.02; 1.01–1.02) |
NA | 3.84e-06 (OR 1.27; 1.15–1.4) |
4.02e-08 (OR 1.2; 1.13–1.28) |
1.04e-14 OR 1.07; 1.05–1.08) |
NA |
| NS5B | 2576(P) | 1.53e-10 (OR 0.98; 0.98–0.99) |
NA | NA | 5.41e-15 (OR 0.77; 0.72–0.82) |
8.39e-12 (OR 0.95; 0.94–0.96) |
1.13e-07 (OR 0.83; 0.77–0.88) |
| NS5B | 2633(S) | NA | 2.33e-09 (OR 1.08; 1.06–1.11) |
NA | NA | NA | NA |
| NS5B | 2729(Q) | 1.19e-12 (OR 0.91; 0.89–0.94) |
1.38e-07 (OR 0.94; 0.92–0.96) |
NA | NA | NA | NA |
| NS5B | 2729(R) | 9.13e-12 (OR 1.09; 1.06–1.12) |
2.22e-09 (OR 1.08; 1.05–1.11) |
NA | NA | NA | NA |
| NS5B | 2755(N) | 2.98e-06 (OR 1.04; 1.02–1.06) |
NA | NA | NA | NA | NA |
| NS5B | 2758(A) | NA | 2.3e-06 (OR 1.05; 1.03–1.07) |
NA | NA | NA | NA |
| NS5B | 2794(Q) | NA | NA | NA | NA | 3.56e-10 (OR 1.08; 1.05–1.1) |
NA |
| NS5B | 2860(G) | NA | 4.63e-12 (OR 1.07; 1.05–1.09) |
NA | NA | NA | NA |
| NS5B | 2937(K) | 8.23e-07 (OR 0.95; 0.93–0.97) |
NA | NA | NA | NA | NA |
| NS5B | 2937(R) | NA | NA | NA | NA | 4.4e-08 (OR 1.08; 1.05–1.11) |
NA |
| NS5B | 2986(H) | NA | NA | NA | NA | 1.03e-06 (OR 0.95; 0.93–0.97) |
NA |
| NS5B | 2986(R) | NA | NA | NA | NA | 2.9e-07 (OR 1.05; 1.03–1.07) |
NA |
| NS5B | 2991(H) | NA | NA | NA | NA | 4.66e-12 (OR 0.88; 0.85–0.91) |
NA |
| NS5B | 2991(Y) | NA | NA | NA | NA | 1.86e-17 (OR 1.17; 1.13–1.22) |
NA |
| NS5B | 3008(F) | 7.47e-08 (OR 1.01; 1.01–1.02) |
NA | NA | NA | NA | NA |