Skip to main content
. 2016 Jan 25;10(1):e0004402. doi: 10.1371/journal.pntd.0004402

Table 4. Frequency of significant mutations (>0.001) identified in patient samples.

GenomeRegion nt Positiona nt Change AA Changeb,c M100 G100 M101 M102 G101 G102 G103 M103 M104 G104 G105 M105 M106 M107 M108 M109 M110 G106 G107 M111
5’UTR 53 A>T 0.106 0.089 0.077 0.086 0.081 0.070 0.078 0.088 0.066 0.072 0.071 0.004 0.004 0.003 0.003 0.003 0.003 0.003 0.002 0.003
nsp1 476 T>A C134S 0.101 0.098 0.090 0.098 0.097 0.106 0.094 0.100 0.107 0.090 0.102 0.017 0.017 0.012 0.010 0.013 0.011 0.012 0.010 0.015
nsp1 479 T>C syn>L 0.988 0.999 0.999 0.985 0.061 0.999 0.010 0.006
nsp1 633 A>C N186T 0.010 0.011 0.010 0.010 0.011 0.009 0.011 0.008 0.103 0.008 0.009 0.004 0.004 0.049 0.005 0.006 0.005 0.013 0.005 0.004
nsp1 667 A>T syn>T 0.071 0.064 0.078 0.040 0.038 0.044 0.041 0.062 0.192 0.040 0.041 0.011 0.012 0.015 0.004 0.005 0.004 0.006 0.005 0.012
nsp1 734 G>C G220R 0.127
nsp1 809 T>G S245A 0.100 0.097 0.089 0.084 0.076 0.092 0.096 0.084 0.079 0.073 0.102 0.051 0.052 0.029 0.041 0.049 0.037 0.046 0.046 0.051
nsp1 864 T>A V263E 0.113 0.009 0.019 0.016 0.007 0.005 0.001 0.001 0.003 0.001 0.004 0.002 0.002 0.002
nsp1 1112 C>T L346F 0.120
nsp1 1525 C>T syn>Y 0.994 0.995 0.996 0.107 0.995
nsp1 1527 G>A S484N 0.100
nsp1 1571 G>A E499K 0.188 0.004
nsp2 2008 C>T syn>H 0.158
nsp2 2038 G>A syn>S 0.002 0.971 0.002 0.981
nsp2 2639 A>T I320F 0.011 0.023 0.012 0.011 0.013 0.010 0.103 0.014 0.014 0.009 0.006 0.005 0.004 0.005 0.007 0.005 0.005
nsp2 2672 C>T R331C 0.110 0.002 0.002
nsp2 2716 A>G syn>T 0.997 0.997 0.995 0.994 0.993 0.995 0.998 0.998 0.997 0.996 0.994 0.997 0.998 0.998 0.998 0.997 0.997 0.998 0.997 0.997
nsp2 2788 T>A syn>I 0.123 0.094 0.133 0.098 0.073 0.087 0.090 0.022 0.021 0.021 0.014 0.012 0.017 0.014 0.013
nsp2 2962 T>C syn>S 0.999
nsp2 3063 T>G I461S 0.065 0.058 0.052 0.053 0.119 0.069 0.018 0.018 0.017 0.022 0.017 0.017 0.022 0.018
nsp2 3196 T>A syn>A 0.005 0.006 0.004 0.006 0.004 0.008 0.002 0.002 0.156 0.002 0.002 0.003 0.002 0.002
nsp2 3519 T>A V613E 0.116 0.129 0.056 0.047 0.096 0.010 0.009 0.014 0.008 0.007 0.008 0.008
nsp2 3591 T>A L637H 0.002 0.003 0.004 0.005 0.001 0.002 0.002 0.002 0.131 0.001
nsp2 3996 G>A G772D 0.504
nsp3 4219 T>A S48R 0.031 0.032 0.037 0.037 0.028 0.033 0.038 0.160 0.180 0.036 0.006 0.005 0.006 0.006 0.003 0.007 0.005 0.006 0.005
nsp3 4221 C>T A49V 0.136 0.002
nsp3 4334 G>A A88T 0.001 0.144
nsp3 4409 G>C G113R 0.671
nsp3 4479 C>T T135M 0.002 0.001 0.463
nsp3 4507 C>A syn>R 0.994 0.995 0.994 0.992 0.995 0.993 0.999 0.993 0.994 0.994 0.994 0.999 0.998 0.998 0.998 0.997 0.997 0.999 0.997 0.997
nsp3 4513 A>G syn>K 1.000 0.999 0.999 0.999 0.998 1.000 0.999 0.998 0.999 0.999 0.999 0.999 0.999 0.999 0.999 0.999 0.999 1.000 0.999 0.999
nsp3 4605 G>A R178Q 0.957 0.003 0.001
nsp3 4606 C>A R178Q 0.959
nsp3 4839 C>T S255F 0.991
nsp3 4864 T>A syn>L 0.021 0.015 0.015 0.008 0.020 0.018 0.011 0.017 0.004 0.002 0.003 0.003 0.004 0.005 0.999 0.089 0.003
nsp3 5090 T>C S340P 0.987
nsp3 5151 A>C D359A 0.047 0.033 0.061 0.093 0.058 0.122 0.195 0.045 0.066 0.055 0.021 0.054 0.039 0.023 0.033 0.026 0.029 0.027 0.031
nsp3 5179 A>C E368D 0.041 0.016 0.058 0.106 0.065 0.133 0.075 0.050 0.034 0.052 0.021 0.034 0.023 0.020 0.024 0.016 0.020 0.016 0.019
nsp3 5190 A>C D359A 0.031 0.017 0.041 0.080 0.045 0.114 0.017 0.039 0.043 0.043 0.022 0.034 0.022 0.019 0.025 0.016 0.017 0.017 0.019
nsp3 5221 T>A syn>L 0.075 0.063 0.105 0.071 0.074 0.039 0.068 0.067 0.075 0.063 0.006 0.005 0.007 0.005 0.005 0.005 0.004 0.005 0.006
nsp3 5298 T>A V408E 0.027 0.018 0.032 0.020 0.151 0.022 0.025 0.020 0.025 0.004 0.003 0.004 0.004 0.005 0.004 0.004 0.004 0.003
nsp3 5305 T>A C410Stop 0.037 0.027 0.042 0.041 0.115 0.026 0.021 0.022 0.022 0.005 0.004 0.004 0.004 0.004 0.004 0.004 0.004 0.002
nsp3 5315 G>A E415K 0.745
nsp3 5325 T>A I417K 0.025 0.034 0.026 0.119 0.036 0.023 0.017 0.023 0.018 0.010 0.012 0.010 0.003 0.005 0.004 0.003 0.004 0.007
nsp3 5334 T>A M420K 0.023 0.024 0.020 0.121 0.033 0.026 0.020 0.019 0.020 0.004 0.004 0.005 0.004 0.004 0.003 0.004 0.003 0.005
nsp3 5376 T>C V435A 0.224 0.003
nsp3 5564 C>T syn>L 0.227
nsp4 5999 T>C S116P 0.008 0.008 0.001 0.001 0.065
nsp4 6075 T>C I141T 0.004 0.105 0.017 0.002
nsp4 6687 T>C L345P 0.179
nsp4 6767 A>C I372L 0.105
nsp4 6805 G>A syn>A 0.078 0.086 0.076 0.057 0.060 0.017 0.120 0.065 0.004 0.002 0.001 0.001
nsp4 6864 T>C I404T 0.969
nsp4 6975 T>A L441Stop 0.179
nsp4 7076 T>G S475A 0.072 0.069 0.079 0.080 0.074 0.625 0.079 0.078 0.075 0.070 0.063 0.030 0.013 0.015 0.013 0.013 0.010 0.013 0.010 0.015
nsp4 7159 T>C syn>A 0.063 0.051 0.063 0.100 0.078 0.090 0.062 0.076 0.082 0.090 0.017 0.016 0.020 0.015 0.020 0.015 0.014 0.018 0.012
E3 8492 A>G Q52R 0.143
E2 8892 T>C syn>I 1.000 1.000 1.000 1.000 0.998 1.000 0.998 1.000
E2 9690 G>A syn>G 0.049 0.068 0.176 0.989 0.069 0.072 0.058
E1 10335 T>A F118L 0.097 0.114 0.084 0.115 0.106 0.090 0.091 0.114 0.096 0.014 0.012 0.014 0.012 0.014 0.011 0.010 0.011 0.015
E1 11046 T>C syn>S 0.002 0.924
3UTR 11302 C>T 0.984
3UTR 11311 T>C 0.979 0.001 0.997
3UTR 11416 T>A 0.015 0.005 0.005 0.006 0.003 0.002 0.008 0.005 0.011 0.002 0.002 0.003 0.001 0.004 0.004 0.005 0.996 0.003 0.006
3UTR 11525 C>T 0.412 0.016 0.003 0.006 0.004 0.464 0.004 0.474 0.021 0.018
3UTR 11775 C>T 0.955 0.980 0.966 0.897 0.997 0.946 0.957 0.965 0.996 0.995 0.872 0.989 0.892 0.982 0.921
3UTR 11776 G>A 0.995 0.997 0.990 0.977 0.997 0.993 0.997 0.993 0.997 0.997 0.890 0.996 0.916 0.994 0.946
3UTR 11791 C>T 0.362 0.586 0.624 0.595 0.640 0.593

a nt = nucleotide

b AA = amino acid

c syn = synonymous

Bold print indicates five novel synonymous sequences changes. The table shows any mutation present above 0.1 in at least one individual, and any mutation above 0.001 found in more than one individual.