1 Introduction

This supplementary document provides a detailed analysis of phenotypic susceptibility data for NRTIs, PIs, and INSTIs using bootstrap LASSO regression.
Mutation frequencies, log₂ fold change distributions, and 95% confidence intervals (CI) are presented.
Original cleaned combination mutation datasets are included.

2 Data Summary

The datasets analyzed include: - NRTI dataset: AZT, TDF, ABC, 3TC susceptibility - PI dataset: NFV, LPV, ATV, DRV susceptibility - INSTI dataset: RAL, EVG, DTG susceptibility

3 Mutation Frequency Tables

Each table includes: - Mutation - Frequency - Mean log₂ Fold Change - 95% Confidence Interval (Lower_CI, Upper_CI)

3.1 Table 1. NRTI Single Mutations (Frequency >5)

nrtimutation_table <- read_xlsx(file.path(output_dir, "NRTI_mutation_table.xlsx"))
kable(nrtimutation_table, caption = "Table 1: NRTI Single Mutations with Frequency >5")
Table 1: NRTI Single Mutations with Frequency >5
Drug Mutation Frequency Mean_Fold Lower_CI Upper_CI
3TC 115F 27 6.33 5.49 7.17
3TC 151M 25 5.55 4.53 6.56
3TC 184I 6 7.45 7.09 7.80
3TC 184V 92 7.17 6.96 7.38
3TC 210W 41 5.04 4.24 5.85
3TC 215F 40 5.48 4.67 6.29
3TC 215Y 42 5.29 4.48 6.09
3TC 41L 67 5.07 4.43 5.71
3TC 65R 19 5.72 4.84 6.60
3TC 67N 73 5.25 4.65 5.84
3TC 70E 6 6.09 4.36 7.81
3TC 70G 8 6.17 4.57 7.77
3TC 70R 52 5.59 4.90 6.27
3TC 70T 6 4.98 2.26 7.70
3TC 74I 24 6.18 5.21 7.15
ABC 115F 27 4.85 4.24 5.46
ABC 151M 25 4.50 3.79 5.21
ABC 184I 6 2.71 0.84 4.59
ABC 184V 92 3.42 3.09 3.74
ABC 210W 41 2.57 2.15 3.00
ABC 215F 40 2.45 2.05 2.85
ABC 215Y 42 2.82 2.34 3.29
ABC 41L 67 2.58 2.23 2.93
ABC 65R 19 3.93 2.90 4.96
ABC 67N 73 2.54 2.19 2.90
ABC 70E 6 2.33 1.48 3.18
ABC 70G 8 3.08 1.81 4.34
ABC 70R 52 2.64 2.27 3.00
ABC 70T 6 4.87 3.36 6.37
ABC 74I 24 3.23 2.54 3.92
AZT 115F 27 4.10 2.20 6.00
AZT 151M 25 7.20 6.01 8.39
AZT 184I 6 3.20 -0.67 7.07
AZT 184V 92 2.89 2.13 3.65
AZT 210W 41 4.99 3.93 6.06
AZT 215F 40 4.18 3.29 5.08
AZT 215Y 42 4.81 3.84 5.78
AZT 41L 67 4.38 3.62 5.13
AZT 65R 19 2.60 0.14 5.06
AZT 67N 73 3.79 3.02 4.56
AZT 70E 6 -1.28 -2.46 -0.09
AZT 70G 8 1.44 -1.58 4.46
AZT 70R 52 4.68 3.86 5.50
AZT 70T 6 3.30 0.00 6.61
AZT 74I 24 4.12 2.76 5.48
TDF 115F 27 1.04 0.42 1.66
TDF 151M 25 1.46 0.83 2.09
TDF 184I 6 0.96 -0.69 2.61
TDF 184V 92 0.26 0.05 0.47
TDF 210W 41 1.08 0.78 1.38
TDF 215F 40 0.72 0.41 1.03
TDF 215Y 42 0.85 0.49 1.21
TDF 41L 67 0.88 0.65 1.11
TDF 65R 19 1.40 0.88 1.93
TDF 67N 73 0.71 0.44 0.97
TDF 70E 6 0.04 -0.61 0.70
TDF 70G 8 0.75 -0.48 1.97
TDF 70R 52 0.78 0.53 1.03
TDF 70T 6 0.72 -0.23 1.66
TDF 74I 24 0.69 0.26 1.11

3.2 Table 2. PI Single Mutations (Frequency >5)

pimutation_table <- read_xlsx(file.path(output_dir, "PI_mutation_table.xlsx"))
kable(pimutation_table, caption = "Table 2: PI Single Mutations with Frequency >5")
Table 2: PI Single Mutations with Frequency >5
Drug Mutation Frequency Mean_Fold Lower_CI Upper_CI
ATV 30N 24 4.15 3.31 4.99
ATV 32I 77 5.38 4.93 5.83
ATV 46I 164 4.76 4.41 5.11
ATV 46L 63 4.76 4.12 5.40
ATV 47V 50 5.30 4.73 5.86
ATV 48M 6 6.82 5.48 8.17
ATV 48V 33 5.93 5.23 6.64
ATV 50L 14 5.55 4.76 6.34
ATV 50V 27 3.51 2.60 4.42
ATV 54A 8 6.77 5.82 7.72
ATV 54L 55 4.76 4.23 5.28
ATV 54M 33 5.36 4.60 6.12
ATV 54S 8 6.48 6.16 6.80
ATV 54T 10 6.70 5.83 7.56
ATV 54V 112 5.16 4.75 5.57
ATV 76V 31 2.68 1.73 3.64
ATV 82A 135 4.95 4.57 5.33
ATV 82C 7 5.48 4.62 6.34
ATV 82F 15 2.93 1.75 4.11
ATV 82L 6 2.55 0.13 4.97
ATV 82T 30 5.20 4.62 5.78
ATV 84V 101 5.66 5.28 6.05
ATV 88G 6 4.03 1.52 6.54
ATV 88S 8 5.07 3.86 6.29
ATV 90M 175 5.35 5.04 5.66
DRV 30N 24 1.64 0.88 2.40
DRV 32I 77 4.98 4.39 5.57
DRV 46I 164 3.47 3.07 3.87
DRV 46L 63 3.21 2.64 3.79
DRV 47V 50 5.08 4.33 5.84
DRV 48M 6 3.65 2.30 5.00
DRV 48V 33 2.00 1.27 2.73
DRV 50L 14 -0.37 -0.92 0.18
DRV 50V 27 5.03 4.16 5.90
DRV 54A 8 2.71 1.29 4.13
DRV 54L 55 4.74 4.12 5.35
DRV 54M 33 5.10 4.22 5.99
DRV 54S 8 2.38 1.01 3.75
DRV 54T 10 3.22 1.74 4.70
DRV 54V 112 2.45 2.08 2.82
DRV 76V 31 3.69 2.68 4.70
DRV 82A 135 2.83 2.43 3.23
DRV 82C 7 3.96 2.54 5.38
DRV 82F 15 2.49 1.49 3.49
DRV 82L 6 1.99 0.07 3.91
DRV 82T 30 1.97 1.16 2.78
DRV 84V 101 4.54 4.08 5.01
DRV 88G 6 1.56 0.43 2.68
DRV 88S 8 0.06 -0.61 0.72
DRV 90M 175 3.54 3.14 3.93
LPV 30N 24 3.76 2.75 4.78
LPV 32I 77 5.67 5.17 6.17
LPV 46I 164 5.54 5.20 5.87
LPV 46L 63 5.28 4.80 5.76
LPV 47V 50 6.18 5.60 6.76
LPV 48M 6 6.92 6.18 7.66
LPV 48V 33 6.65 5.98 7.33
LPV 50L 14 1.14 0.14 2.14
LPV 50V 27 6.38 5.67 7.08
LPV 54A 8 7.38 6.84 7.93
LPV 54L 55 4.82 4.28 5.35
LPV 54M 33 5.66 5.01 6.30
LPV 54S 8 7.34 6.75 7.93
LPV 54T 10 6.74 5.85 7.64
LPV 54V 112 5.99 5.71 6.27
LPV 76V 31 6.01 5.35 6.67
LPV 82A 135 5.71 5.36 6.05
LPV 82C 7 6.85 6.55 7.16
LPV 82F 15 5.73 4.93 6.54
LPV 82L 6 2.92 0.61 5.23
LPV 82T 30 5.26 4.54 5.98
LPV 84V 101 5.80 5.48 6.11
LPV 88G 6 3.45 0.99 5.90
LPV 88S 8 2.03 0.48 3.57
LPV 90M 175 5.42 5.10 5.74
NFV 30N 24 6.95 6.25 7.65
NFV 32I 77 4.69 4.34 5.04
NFV 46I 164 4.87 4.58 5.15
NFV 46L 63 5.08 4.56 5.61
NFV 47V 50 4.67 4.19 5.14
NFV 48M 6 6.08 4.58 7.59
NFV 48V 33 5.88 5.22 6.54
NFV 50L 14 1.62 0.79 2.44
NFV 50V 27 4.37 3.56 5.18
NFV 54A 8 7.07 6.27 7.88
NFV 54L 55 4.87 4.43 5.31
NFV 54M 33 4.85 4.28 5.42
NFV 54S 8 6.43 5.73 7.13
NFV 54T 10 6.82 6.19 7.45
NFV 54V 112 5.45 5.13 5.77
NFV 76V 31 3.52 2.84 4.21
NFV 82A 135 4.95 4.62 5.28
NFV 82C 7 5.80 4.96 6.63
NFV 82F 15 4.70 3.81 5.59
NFV 82L 6 2.44 0.30 4.59
NFV 82T 30 4.76 4.32 5.20
NFV 84V 101 5.04 4.72 5.36
NFV 88G 6 3.47 1.53 5.42
NFV 88S 8 5.35 3.94 6.76
NFV 90M 175 5.42 5.17 5.66

3.3 Table 3. INSTI Single Mutations (Frequency >5)

instimutation_table <- read_xlsx(file.path(output_dir, "INSTI_mutation_table.xlsx"))
kable(instimutation_table, caption = "Table 3: INSTI Single Mutations with Frequency >5")
Table 3: INSTI Single Mutations with Frequency >5
Drug Mutation Frequency Mean_Fold Lower_CI Upper_CI
DTG 138K 9 3.12 1.71 4.53
DTG 140S 7 1.51 0.33 2.69
DTG 148R 10 2.06 1.32 2.81
EVG 138K 9 5.81 4.01 7.61
EVG 140S 7 5.54 3.55 7.52
EVG 148R 10 7.05 6.87 7.23
RAL 138K 9 5.61 4.02 7.19
RAL 140S 7 5.13 2.50 7.76
RAL 148R 10 6.28 5.77 6.78

4 LASSO Bootstrap Coefficient Estimates

Figures show estimated LASSO regression coefficients (log₂ fold units) for each drug class.

4.1 Figure 1. LASSO Estimates for NRTIs

knitr::include_graphics(file.path(output_dir, "NRTI_final_plot.pdf"))

Figure 1: LASSO Coefficient Estimates for NRTIs

4.2 Figure 2. LASSO Estimates for PIs

knitr::include_graphics(file.path(output_dir, "PI_final_plot.pdf"))

Figure 2: LASSO Coefficient Estimates for PIs

4.3 Figure 3. LASSO Estimates for INSTIs

knitr::include_graphics(file.path(output_dir, "INSTI_final_plot.pdf"))

Figure 3: LASSO Coefficient Estimates for INSTIs

5 Supplementary Tables

The following supplementary tables list the cleaned combination mutation datasets (MutPatterns + NumSeqs + Fold columns) with NA rows and “None” MutPatterns removed.

5.1 Supplementary Table S1. Cleaned Combination Mutations for NRTIs

nrticombination_table <- read_xlsx(file.path(output_dir, "NRTI_combination_cleaned.xlsx"))
kable(nrticombination_table, caption = "Supplementary Table S1: Cleaned Combination Mutations for NRTIs")
Supplementary Table S1: Cleaned Combination Mutations for NRTIs
MutPatterns NumSeqs AZT_n AZT_fold TDF_n TDF_fold ABC_n ABC_fold 3TC_n 3TC_fold
184V 16804 150 0.4 86 0.5 149 3.2 206 200.0
67N,70R,184V 2876 50 2.8 42 1.0 47 4.1 71 200.0
41L,67N,184V,210W,215Y 2567 143 30.0 121 1.5 131 7.4 182 200.0
41L,184V,210W,215Y 2242 115 11.0 97 1.3 109 6.9 153 200.0
41L,184V,215Y 1959 62 4.5 43 1.0 61 5.2 85 200.0
65R,184V 1858 19 0.4 19 1.3 19 8.7 29 200.0
70R,184V 1593 20 1.4 13 0.8 21 3.6 30 200.0
41L 1478 12 1.0 10 1.0 11 1.0 17 1.6
41L,67N,210W,215Y 1375 70 321.0 60 3.9 58 5.8 98 7.0
67N,70R,184V,215F 1168 20 5.3 13 0.8 20 5.5 20 200.0
41L,210W,215Y 1113 39 124.0 35 3.1 36 3.5 59 3.2
184V,215Y 1019 19 2.6 12 0.6 19 5.0 24 200.0
67N,70R 1001 31 28.0 27 1.9 29 1.8 42 2.3
65R 992 22 0.6 19 1.8 21 2.5 31 8.8
70R 748 20 5.3 18 1.2 21 1.2 28 1.4
41L,215Y 713 21 12.0 16 1.4 18 2.5 27 2.0
67N 710 12 1.1 10 0.8 11 0.9 17 2.2
41L,184V 690 7 0.5 6 0.4 7 4.3 11 200.0
41L,67N,70R,184V,215F 689 31 46.0 24 1.7 31 6.1 42 200.0
184I 659 18 0.3 17 0.5 17 1.9 32 101.0
184V,215F 611 4 2.2 4 0.8 4 4.6 7 200.0
41L,184V,215F 583 10 3.1 4 0.8 10 5.6 9 119.0
67N,70R,215F 578 31 102.0 24 2.6 30 2.5 38 3.8
67N,184V 537 7 0.4 7 0.4 7 2.7 11 200.0
65R,115F,184V 518 1 0.6 1 1.9 1 123.0 NA NA
115F,184V 512 10 0.6 10 0.7 9 12.0 15 200.0
41L,67N,184V,215Y 503 13 7.4 7 1.0 13 5.7 15 200.0
41L,210W 447 6 1.0 6 0.9 6 1.0 8 1.2
70E,184V 440 6 0.2 6 0.6 6 3.4 10 200.0
215Y 411 15 8.1 14 1.4 12 1.6 17 2.0
41L,67N,70R,184V,215Y 385 10 7.8 8 1.6 10 5.2 11 200.0
41L,67N,70R,184V,210W,215Y 362 15 23.0 12 1.8 14 7.2 19 200.0
65R,184I 348 3 0.3 3 1.1 3 3.1 6 200.0
41L,74I,184V,210W,215Y 346 13 16.0 12 1.3 13 7.6 16 200.0
41L,67N,70R,215F 319 20 387.0 16 4.2 18 3.9 28 5.5
41L,67N,74I,184V,210W,215Y 312 19 24.0 17 1.6 18 8.7 28 200.0
41L,184V,210W 306 3 2.9 3 5.0 3 13.0 3 94.0
74I,184V 304 2 0.2 2 0.4 2 2.8 3 200.0
210W 303 3 1.1 1 0.8 3 0.8 4 1.3
41L,67N,70R,74I,184V,215F 257 6 39.0 5 2.3 6 14.0 8 200.0
41L,67N,210W 234 6 1.4 6 0.9 6 1.2 7 3.5
70R,184V,215F 217 4 17.0 4 1.3 4 5.5 7 200.0
67N,70R,184V,215Y 214 8 4.5 8 1.1 8 5.0 12 200.0
184V,210W,215Y 211 6 2.5 6 0.8 6 4.3 10 200.0
41L,67N,215Y 210 11 64.0 4 3.8 11 2.5 12 3.6
151M,184V 197 4 126.0 2 0.8 3 21.0 4 200.0
65R,115F 183 2 0.3 2 1.8 2 5.8 3 200.0
67N,70R,215Y 181 3 36.0 2 2.5 3 2.7 5 3.9
41L,67N,70R,210W,215Y 175 7 470.0 7 3.6 6 5.5 11 5.6
41L,184V,210W,215F 172 3 8.0 3 0.8 2 7.8 4 174.0
41L,67N,70R,215Y 166 5 55.0 2 3.5 4 2.5 6 4.4
41L,67N,70R,184V 165 2 27.0 2 2.0 2 3.5 4 129.0
151M 156 12 8.6 11 1.4 11 6.2 17 2.9
67N,70E,184V 151 1 0.3 1 0.8 1 7.2 1 84.0
41L,215F 150 1 50.0 1 3.2 1 2.6 NA NA
215F 144 3 2.9 3 0.9 3 1.0 4 1.4
65R,70T,184V 142 1 2.3 1 1.0 1 6.4 2 200.0
67N,70R,74I,184V,215F 141 7 9.6 7 1.1 7 7.2 6 123.0
41L,67N,184V,215F 131 5 1.6 5 0.8 5 5.9 7 200.0
41L,70R,184V 129 2 7.8 2 1.1 2 3.0 4 200.0
41L,74I,184V,215Y 126 3 7.2 3 1.1 3 4.7 4 29.0
41L,67N,70R,184V,210W,215F 119 5 61.0 5 1.7 5 5.7 6 82.0
41L,70R,184V,215F 119 5 163.0 5 2.5 5 5.1 5 122.0
41L,67N,184I,210W,215Y 115 1 668.0 1 4.5 1 13.0 2 200.0
67N,184V,210W,215Y 105 5 7.2 5 1.2 5 6.4 6 200.0
210W,215Y 101 4 31.0 3 1.3 4 2.1 4 2.5
70R,215F 98 3 31.0 1 2.3 3 1.8 4 2.5
115F,151M,184V 98 1 584.0 1 1.6 1 20.0 2 200.0
67N,184V,215F 97 1 0.9 1 0.5 1 3.0 2 200.0
67N,70R,74I,184V 93 2 16.0 2 1.5 2 6.1 3 200.0
41L,67N,184V,210W,215F 93 6 189.0 6 2.7 6 9.4 10 200.0
41L,67N,74I,210W,215Y 90 5 2400.0 5 6.2 5 7.2 10 10.0
65R,151M 90 5 400.0 5 7.7 3 21.0 5 62.0
70E,115F,184V 87 1 0.2 1 0.9 1 10.0 2 200.0
70E 82 2 0.2 3 0.9 3 1.4 5 5.3
41L,67N,184V 80 2 0.5 2 0.4 2 2.5 2 200.0
70N 76 1 0.8 1 1.1 1 1.1 1 1.4
41L,67N 75 5 1.1 5 0.8 5 1.0 8 1.6
41L,67N,70R,210W,215F 68 6 158.0 6 2.9 5 4.0 7 7.1
65R,74I,184V 66 1 0.4 1 1.4 1 123.0 NA NA
70Q,184V 65 2 0.2 2 0.5 2 3.4 3 200.0
65R,151M,184V 64 1 1698.0 1 5.9 1 123.0 NA NA
67N,215Y 64 3 7.3 2 1.1 2 2.1 4 4.5
74I 61 2 0.9 2 1.0 2 1.0 2 0.8
67N,210W,215Y 57 1 101.0 1 5.1 1 4.7 NA NA
41L,70R,74I,184V,215F 56 5 3.5 5 0.9 5 5.6 8 200.0
41L,67N,70R,74I,215F 55 3 63.0 3 2.0 3 4.0 6 4.2
65R,67N 54 1 0.4 1 1.3 1 3.0 2 14.0
67N,215F 54 3 7.2 2 1.2 2 1.9 4 4.3
41L,67N,215F 51 1 38.0 1 2.1 1 2.0 1 3.4
65N 48 1 1.7 1 2.1 1 7.3 NA NA
41L,210W,215F 47 3 217.0 2 4.1 1 3.2 4 3.1
41L,70R,184V,215Y 47 2 70.0 2 2.5 2 7.5 3 200.0
41L,67N,70R,74I,184V,210W,215Y 45 4 369.0 4 2.3 4 10.0 7 200.0
41L,70R,215F 43 1 11.0 1 1.1 1 3.2 2 3.6
70G,184V 38 4 0.2 4 0.6 4 5.8 8 200.0
74I,184V,215Y 37 1 0.6 1 0.3 1 4.5 2 200.0
70R,74I,184V 36 2 52.0 2 2.1 2 8.9 3 200.0
41L,67N,210W,215F 35 1 36.0 1 1.9 1 3.6 1 7.4
67N,70R,151M,184V 35 1 9.1 1 0.8 1 12.0 2 200.0
115F 34 1 0.9 1 1.3 1 2.8 1 1.6
67N,70R,151M 34 1 18.0 1 1.6 1 3.1 2 3.7
67N,151M,184V 34 2 4.6 1 0.3 2 8.5 3 200.0
41L,67N,74I,184V,215Y 33 1 4.3 1 0.9 1 96.0 NA NA
67N,210W 32 1 0.4 1 0.5 1 0.9 2 3.6
67N,70G,184V 29 2 0.2 2 0.6 2 4.0 4 200.0
41L,67N,74I,184V,215F 28 1 20.0 1 2.0 1 12.0 2 200.0
41L,74I,210W,215Y 25 2 271.0 2 2.9 2 5.8 2 7.4
41L,70R,215Y 24 1 177.0 1 2.2 1 4.9 2 3.3
41L,74I,184V,210W,215F 24 1 685.0 1 3.4 1 19.0 2 200.0
65R,70R,115F,151M 24 1 2400.0 1 11.0 1 20.0 1 89.0
67N,70G,184V,215F 22 3 0.8 1 0.8 3 7.1 3 200.0
41L,70R,184V,210W,215Y 22 1 149.0 1 3.3 1 9.9 2 200.0
67N,70R,184I 22 1 5.2 1 1.0 1 3.4 2 200.0
115F,151M 21 1 5.2 1 20.0 1 15.0 NA NA
115F,184V,215Y 19 2 0.6 2 0.4 2 18.0 2 73.0
41L,115F,184V,215Y 19 1 0.8 1 0.7 1 98.0 NA NA
65N,115F 17 1 2.6 1 7.4 1 23.0 NA NA
70R,115F,184V 17 1 0.7 1 0.7 1 12.0 1 80.0
115F,184V,215F 16 3 2.2 3 0.7 3 16.0 4 200.0
65R,70R 15 1 0.2 1 1.2 1 3.6 1 8.2
41L,67N,74I,184V,210W,215F 14 1 77.0 1 7.0 1 200.0 NA NA
65R,70T,115F,151M,184V 13 1 985.0 1 7.5 1 100.0 NA NA
70R,151M,184V 13 1 33.0 1 0.8 1 18.0 1 67.0
67N,70R,184V,210W 13 1 21.0 1 2.0 1 14.0 1 65.0
67N,70R,184V,210W,215F 12 1 2.6 1 1.0 1 4.9 1 80.0
67N,70R,184I,215F 12 1 5.2 1 0.9 1 2.3 2 200.0
67N,70R,115F,184V 12 1 0.5 1 0.5 1 100.0 NA NA
41L,70R,184V,210W 12 1 2.7 1 1.1 1 6.6 1 81.0
65R,70R,115F,151M,184V 12 1 2400.0 1 7.5 1 170.0 2 200.0
41L,67N,70R,74I,210W,215F 11 1 58.0 1 2.2 1 4.4 NA NA
70G,115F,151M,184V 11 2 245.0 1 2.4 2 20.0 2 200.0
70N,115F,151M,184V 10 1 987.0 1 2.2 1 20.0 1 200.0
41L,70T,184V,210W,215Y 10 1 5.7 1 1.1 1 11.0 1 72.0
41L,67N,70Q,210W,215Y 10 1 788.0 1 5.7 1 8.6 1 10.0
67N,70R,115F,151M,184V 10 1 802.0 1 1.8 1 28.0 1 54.0
67N,70E,184V,215F 8 1 0.9 1 1.0 1 5.3 1 81.0
65R,70E 8 1 2.3 1 3.1 1 8.8 NA NA
67N,70R,74I,115F,184V 8 2 1.8 2 1.0 2 14.0 2 200.0
41L,67N,151M,210W,215Y 7 1 154.0 1 2.6 1 4.0 2 6.2
67N,70G,215F 6 1 0.8 1 0.9 1 6.1 NA NA
41L,67N,70R,74I,210W 6 1 22.0 1 3.5 1 4.1 NA NA
70S,115F,151M,184V 5 1 252.0 1 2.0 1 25.0 1 71.0
65R,67N,115F,151M 5 1 1109.0 1 7.8 1 117.0 NA NA
41L,67N,151M,215F 4 1 39.0 1 8.0 1 6.6 NA NA
41L,65R,210W 4 1 0.4 1 2.1 1 2.5 2 11.0
65R,184V,210W 4 1 0.4 1 1.4 1 8.6 1 87.0
70T,115F,151M,184V 4 1 8.5 1 1.0 1 60.0 1 1.0
41L,67N,70R,151M 4 1 47.0 1 1.3 1 2.6 1 3.2
41L,67N,70G,215F 4 1 2.5 1 1.5 1 2.6 2 6.2
70T,151M,184V 3 1 42.0 1 1.0 1 11.0 1 69.0
41L,67N,70N,184V,215Y 3 1 8.5 1 1.8 1 4.6 2 200.0
70N,115F,151M,184V,215Y 3 1 2400.0 1 3.2 1 200.0 2 200.0
67N,70G,115F,151M,184I,215Y 3 2 372.0 2 24.0 2 133.0 NA NA
65R,67N,70G 3 1 0.5 1 2.8 1 3.7 2 14.0
70N,184V,215Y 2 1 0.6 1 0.6 1 3.0 1 71.0
70R,184V,210W,215F 2 1 2400.0 1 7.2 1 27.0 2 200.0
41L,70R,74I,115F,184V,215F 2 1 28.0 1 1.2 1 8.2 1 62.0
41L,67N,115F,184V 2 1 0.3 1 0.7 1 24.0 1 80.0
41L,70T,184V 2 1 0.2 1 2.4 1 132.0 NA NA

5.2 Supplementary Table S2. Cleaned Combination Mutations for PIs

picombination_table <- read_xlsx(file.path(output_dir, "PI_combination_cleaned.xlsx"))
kable(picombination_table, caption = "Supplementary Table S2: Cleaned Combination Mutations for PIs")
Supplementary Table S2: Cleaned Combination Mutations for PIs
MutPatterns NumSeqs NFV_n NFV_fold SQV_n SQV_fold IDV_n IDV_fold FPV_n FPV_fold ATV_n ATV_fold LPV_n LPV_fold TPV_n TPV_fold DRV_n DRV_fold
90M 2908 60 7.3 61 3.2 61 3.1 57 1.4 43 3.1 52 1.6 34 1.1 29 0.8
30N 1989 48 39.0 46 1.5 47 1.4 41 0.8 32 2.5 29 1.0 14 1.1 10 0.8
46I 970 3 15.0 3 0.9 3 4.4 3 2.1 2 4.5 1 1.7 1 0.9 1 0.5
46L 857 2 8.2 2 1.5 2 2.6 2 1.1 1 2.4 2 1.6 NA NA NA NA
46I,90M 855 44 18.0 44 4.2 42 8.1 37 2.4 25 3.8 31 2.5 21 0.9 14 0.7
54V,82A 735 28 10.0 28 2.2 27 9.6 26 2.1 17 4.2 24 16.0 13 2.0 10 1.6
54V,82A,90M 701 31 43.0 31 20.0 31 22.0 29 3.3 12 14.0 29 37.0 9 1.8 6 1.2
46I,54V,82A 623 24 16.0 24 1.8 22 15.0 20 3.6 8 5.8 18 34.0 5 0.9 4 1.0
46L,54V,82A 554 24 35.0 24 6.7 23 19.0 21 5.5 13 31.0 21 48.0 14 1.1 8 1.7
46I,84V,90M 496 36 48.0 34 42.0 35 28.0 36 7.7 22 23.0 30 17.0 14 2.0 8 4.0
46L,54V,82A,90M 470 23 40.0 23 13.0 22 29.0 23 9.2 13 22.0 21 67.0 10 4.5 9 4.4
84V,90M 460 26 19.0 26 25.0 27 11.0 26 4.5 14 15.0 25 6.4 11 2.1 8 2.1
82A 456 8 2.1 8 0.8 8 2.1 8 1.0 7 1.9 8 2.2 3 0.4 NA NA
46I,54V,84V,90M 433 26 82.0 23 134.0 26 56.0 26 21.0 17 155.0 25 75.0 17 5.1 14 12.0
46I,54V,82A,90M 414 28 42.0 28 22.0 28 28.0 28 6.4 22 27.0 28 64.0 20 2.0 14 1.8
88S 266 16 8.3 16 1.2 16 2.5 16 0.1 5 8.3 4 1.3 2 1.0 2 0.4
46I,54V,76V,82A 265 11 8.3 11 1.3 6 33.0 11 6.7 11 1.2 11 86.0 4 0.6 3 4.6
54V,84V,90M 236 15 60.0 15 101.0 15 52.0 15 20.0 11 86.0 12 55.0 11 7.1 11 8.1
54V,90M 224 3 34.0 3 60.0 3 5.0 3 1.3 1 72.0 2 28.0 1 23.0 1 2.1
50L 191 16 0.4 9 0.3 16 0.3 16 0.3 20 7.0 6 0.3 1 0.5 1 0.4
30N,90M 186 15 74.0 15 6.0 15 2.8 15 1.3 5 4.8 5 1.8 1 0.5 1 0.4
84V 186 12 2.6 12 2.8 11 2.1 11 2.5 6 2.9 11 2.6 5 2.6 4 1.5
54V 169 2 18.0 2 8.1 2 6.2 2 3.0 2 8.6 2 5.4 1 2.7 1 0.6
30N,46I 147 5 25.0 5 0.6 5 1.2 5 0.8 3 1.5 4 0.8 2 0.4 1 0.5
46I,88S 145 9 19.0 9 1.4 9 6.1 8 0.2 2 11.0 3 0.8 1 1.6 1 0.8
46L,82A 142 3 6.1 3 1.3 3 7.4 3 5.8 2 2.5 3 7.0 NA NA NA NA
46I,84V 131 1 13.0 1 11.0 1 5.6 1 6.7 1 14.0 1 14.0 1 11.0 NA NA
46L,90M 126 8 15.0 8 3.8 8 6.8 8 1.7 4 6.5 6 2.7 3 0.7 3 0.9
82A,90M 125 2 6.1 2 1.6 2 7.1 2 1.6 1 5.5 2 2.7 NA NA NA NA
48V,54V,82A 112 8 22.0 8 115.0 8 17.0 8 1.9 8 20.0 8 27.0 5 0.9 4 0.6
46I,54V,82F,90M 108 9 106.0 9 7.4 9 104.0 9 24.0 5 62.0 9 89.0 5 4.4 4 11.0
46I,82A 105 1 67.0 1 22.0 1 41.0 1 7.8 1 43.0 1 45.0 NA NA NA NA
54L,84V,90M 104 11 27.0 11 86.0 10 9.3 11 30.0 10 26.0 11 16.0 7 1.2 7 11.0
32I,46I,47V,54M,82A,90M 91 6 34.0 6 11.0 6 93.0 6 149.0 6 53.0 6 153.0 6 9.3 6 79.0
46L,54V,84V,90M 91 11 89.0 11 95.0 10 62.0 11 35.0 11 90.0 11 103.0 9 5.5 6 13.0
46I,47V,54V,84V,90M 87 4 126.0 2 85.0 3 148.0 4 44.0 4 125.0 4 154.0 4 9.8 3 13.0
46I,76V 85 1 3.0 1 0.6 1 13.0 1 4.4 NA NA NA NA NA NA NA NA
32I,46I,82A,90M 84 6 25.0 6 4.5 5 21.0 6 12.0 6 20.0 6 15.0 3 1.5 2 46.0
46I,50V,54V,82A 82 3 6.0 3 4.3 3 5.6 3 31.0 3 2.2 3 101.0 3 0.5 3 24.0
46L,54V,82A,84V 80 11 24.0 11 79.0 10 25.0 11 16.0 10 33.0 11 41.0 7 9.8 3 18.0
48V,54T,82A 80 5 92.0 4 750.0 5 76.0 5 4.9 5 78.0 5 35.0 3 0.7 2 1.0
46I,54V,82A,84V,90M 79 4 53.0 3 61.0 4 28.0 4 24.0 3 58.0 4 119.0 3 10.0 2 9.7
46I,54V,82A,84V 79 2 25.0 2 59.0 2 12.0 2 16.0 2 36.0 2 99.0 1 7.7 NA NA
54V,82A,84V,90M 78 4 47.0 4 97.0 4 23.0 4 10.0 1 59.0 4 52.0 1 3.7 NA NA
46I,54V,84V 77 9 54.0 9 74.0 9 42.0 9 19.0 5 78.0 9 90.0 3 2.0 3 15.0
48V,54V,82A,90M 76 10 35.0 10 254.0 10 28.0 10 1.8 5 27.0 10 32.0 5 0.5 3 0.4
46I,50V,54V,82A,90M 75 2 154.0 1 25.0 2 60.0 1 37.0 1 45.0 1 252.0 2 1.4 1 15.0
32I,46I,47V,54L,84V,90M 75 8 50.0 8 74.0 8 26.0 8 187.0 8 172.0 8 184.0 8 6.3 6 499.0
54L 75 2 2.6 2 1.4 2 1.4 2 7.7 2 1.6 2 2.7 2 1.2 2 2.4
46I,54V,76V,82A,90M 75 1 50.0 1 7.6 1 21.0 1 2.8 1 219.0 NA NA NA NA NA NA
54L,90M 74 5 8.1 5 3.9 5 1.9 4 14.0 4 12.0 5 2.2 4 1.4 3 3.4
54V,82F,90M 73 3 34.0 4 8.8 2 51.0 4 13.0 3 11.0 4 54.0 2 8.1 2 6.3
50L,82A 69 1 0.7 1 0.3 1 0.8 1 0.7 1 12.0 1 0.7 1 0.4 1 0.2
32I,46I,47V,54M,90M 66 2 18.0 2 5.8 2 15.0 2 168.0 2 16.0 2 129.0 2 6.5 2 134.0
32I 64 3 7.7 3 2.6 3 3.2 3 2.9 3 4.3 3 1.6 3 2.1 3 2.1
46L,54V,82A,84V,90M 64 9 42.0 9 41.0 9 33.0 9 15.0 5 72.0 8 88.0 4 18.0 2 12.0
46I,54V,82S 63 1 60.0 1 33.0 1 51.0 1 4.2 1 52.0 1 91.0 1 0.9 NA NA
46L,84V,90M 63 7 20.0 7 29.0 6 12.0 7 8.6 6 13.0 6 8.7 6 4.5 6 4.0
82L 61 5 0.9 5 0.7 5 0.6 5 1.0 5 1.2 5 0.6 5 1.4 5 1.1
82F 61 5 4.3 5 0.4 4 3.8 3 2.0 2 2.8 2 5.0 2 0.8 2 0.8
32I,46I,82A 61 3 11.0 3 0.8 3 10.0 3 4.8 2 3.5 2 5.0 NA NA NA NA
46I,76V,84V 58 2 5.8 2 2.8 2 21.0 2 19.0 2 33.0 NA NA NA NA NA NA
32I,46I,47V,82A 58 2 13.0 2 1.3 2 22.0 2 13.0 1 48.0 2 55.0 2 1.1 1 5.1
46I,47V,54V,82A 57 1 16.0 1 4.8 1 10.0 1 8.7 1 6.8 1 61.0 1 2.9 NA NA
32I,46I,47V,54V,82A,90M 56 6 44.0 6 12.0 5 35.0 6 23.0 5 15.0 6 94.0 5 2.5 3 5.6
50V 56 4 3.0 4 1.6 4 1.2 4 14.0 2 1.4 4 6.7 NA NA NA NA
54V,82T,90M 56 5 30.0 5 7.4 5 21.0 5 2.4 3 27.0 5 13.0 2 13.0 2 1.2
32I,46I,54V,82A,90M 56 1 28.0 1 23.0 1 20.0 1 14.0 1 17.0 1 22.0 1 2.1 1 4.4
46I,54V,82T,90M 54 6 54.0 6 19.0 6 28.0 5 2.9 4 31.0 6 38.0 4 9.6 3 1.1
46L,50L,82A 54 4 5.4 4 1.7 4 2.9 4 9.2 4 67.0 4 6.2 4 2.6 4 2.5
32I,46I,47V,82A,90M 54 1 72.0 1 33.0 1 89.0 1 83.0 1 700.0 1 500.0 1 15.0 1 44.0
46I,50V 53 3 3.3 3 1.4 2 1.4 3 21.0 1 0.9 3 15.0 NA NA NA NA
54V,82A,84V 53 6 19.0 6 41.0 6 9.1 6 13.0 4 22.0 6 39.0 3 5.1 2 4.3
46I,54V,82T,84V 53 5 68.0 5 209.0 5 156.0 4 12.0 4 116.0 5 74.0 3 25.0 1 4.5
50L,90M 52 1 1.4 1 1.7 1 0.9 1 1.0 1 16.0 1 0.2 1 0.5 1 0.5
54V,82T 52 8 27.0 8 4.8 8 24.0 6 1.0 1 15.0 3 3.4 NA NA NA NA
46L,82A,90M 51 3 9.6 3 4.2 3 11.0 3 4.0 2 18.0 3 15.0 2 18.0 1 1.2
46I,54V,90M 49 1 29.0 1 1000.0 1 27.0 1 13.0 1 228.0 1 61.0 1 3.8 1 5.6
54V,82F 48 2 57.0 2 3.4 2 35.0 2 16.0 2 10.0 2 71.0 1 6.6 NA NA
46L,54V,76V,82A 48 3 17.0 3 2.5 3 35.0 3 15.0 2 2.0 3 120.0 1 0.6 NA NA
54V,84V 47 1 62.0 1 267.0 1 34.0 1 76.0 1 120.0 1 109.0 1 5.1 NA NA
30N,54V,90M 47 5 200.0 5 46.0 5 8.4 5 2.3 1 13.0 1 14.0 1 4.5 1 1.4
32I,46I,47V,90M 46 5 6.2 5 1.1 5 4.5 5 12.0 4 14.0 4 15.0 4 3.1 4 5.2
46L,48V,54V,82A 45 1 99.0 1 1000.0 1 90.0 1 9.0 1 161.0 1 126.0 1 0.5 1 1.4
46I,54L,84V,90M 45 2 74.0 2 1000.0 2 25.0 2 47.0 2 74.0 2 48.0 2 3.5 2 21.0
46I,54V,82T,84V,90M 45 8 80.0 7 106.0 6 97.0 8 13.0 7 132.0 8 96.0 5 27.0 3 5.1
46I,54V,82T 44 3 13.0 3 7.4 3 35.0 3 4.0 3 17.0 3 64.0 3 0.8 3 1.1
32I,46L,82A 42 3 4.5 3 0.7 3 4.3 3 1.6 1 5.2 NA NA NA NA NA NA
46I,54M,84V,90M 42 4 59.0 4 56.0 4 24.0 4 47.0 1 82.0 2 70.0 NA NA NA NA
54V,76V,82A 42 6 8.7 6 2.2 5 23.0 6 9.1 6 3.3 6 84.0 3 2.1 2 2.7
32I,47V 41 1 3.9 1 1.5 1 1.7 1 2.5 1 6.3 1 4.0 1 1.5 1 1.3
48V,90M 41 2 5.3 2 19.0 2 5.0 2 2.0 1 1.2 NA NA NA NA NA NA
46I,50L,82A 40 1 1.1 1 0.4 1 0.5 1 1.5 1 19.0 1 1.5 1 0.6 1 0.4
32I,46I,47V,54M,84V,90M 40 7 47.0 7 22.0 7 25.0 6 181.0 7 91.0 7 183.0 5 30.0 5 500.0
54L,82A,90M 39 3 25.0 3 17.0 3 9.7 3 15.0 3 27.0 3 17.0 2 4.5 NA NA
46I,54V,76V,84V 39 1 12.0 1 6.8 1 22.0 1 45.0 1 6.0 1 159.0 1 1.9 1 22.0
46I,82T 39 4 13.0 4 1.8 4 13.0 4 2.8 3 6.5 3 16.0 3 1.8 1 1.8
48V,54V,82A,84V 39 4 18.0 4 583.0 4 12.0 4 6.0 2 70.0 2 80.0 2 2.0 1 2.5
32I,46I,47V,54M,82A 36 6 18.0 6 1.2 6 20.0 6 84.0 6 8.3 6 121.0 5 5.3 3 33.0
48V,54S,82A 36 3 119.0 3 1000.0 3 154.0 3 15.0 2 128.0 3 117.0 3 1.5 3 3.9
46I,82T,90M 35 5 27.0 5 17.0 5 28.0 5 3.9 3 19.0 5 18.0 2 3.5 2 1.1
46L,54V,76V,82A,90M 34 1 6.8 1 3.8 1 22.0 1 5.6 1 0.7 1 33.0 1 0.9 1 2.5
32I,46I,47V,54L,82A,90M 33 4 44.0 4 8.2 4 26.0 4 134.0 2 38.0 4 218.0 1 2.7 NA NA
46L,54L,82A,90M 31 2 12.0 2 3.5 2 6.5 2 23.0 2 8.9 2 10.0 2 1.0 1 8.1
32I,47V,54M,90M 31 2 63.0 2 52.0 2 34.0 2 152.0 2 76.0 2 130.0 2 10.0 NA NA
46L,54V,84V 31 2 426.0 2 629.0 2 347.0 2 61.0 2 504.0 2 113.0 2 125.0 1 25.0
88S,90M 31 3 97.0 3 34.0 3 17.0 3 0.7 1 67.0 2 10.0 NA NA NA NA
46I,54A,82A 30 1 200.0 1 38.0 1 197.0 1 12.0 1 63.0 1 219.0 1 1.3 1 1.8
46I,82A,90M 30 3 20.0 3 4.0 3 25.0 3 7.0 2 11.0 3 14.0 1 2.1 1 5.0
46I,54V,76V,82F 29 1 16.0 1 0.9 1 46.0 1 9.5 1 1.0 1 112.0 NA NA NA NA
54M 29 1 4.7 1 1.9 1 2.0 1 12.0 1 3.4 1 2.9 NA NA NA NA
54L,84V 29 2 8.2 2 27.0 2 2.6 2 28.0 2 14.0 2 9.4 2 1.6 NA NA
46I,76V,84V,90M 28 2 12.0 2 54.0 2 42.0 2 160.0 2 19.0 2 162.0 1 1.1 1 109.0
54M,90M 28 2 17.0 2 13.0 2 9.4 2 38.0 2 17.0 2 10.0 2 5.4 2 7.8
30N,46I,54V,82A 28 1 600.0 1 23.0 1 46.0 1 34.0 1 44.0 1 500.0 1 2.2 1 7.8
46I,82F,90M 28 2 50.0 2 1.8 2 37.0 2 13.0 2 12.0 2 37.0 NA NA NA NA
46I,88S,90M 27 2 67.0 2 6.7 2 16.0 2 0.7 1 16.0 2 2.3 2 1.0 2 1.0
46L,84V 27 1 4.3 1 1.8 1 3.2 1 1.6 1 1.9 NA NA NA NA NA NA
32I,46I,47V 27 1 8.0 1 1.0 1 16.0 1 6.6 1 9.0 1 8.7 1 1.6 1 2.5
46I,82A,84V 27 1 4.4 1 3.4 1 3.8 1 6.3 1 3.1 1 7.9 1 1.3 1 1.3
48V,54T,82A,90M 27 1 165.0 1 7.6 1 151.0 1 1.3 NA NA NA NA NA NA NA NA
54V,82T,84V,90M 26 2 72.0 1 91.0 2 61.0 2 11.0 1 187.0 1 98.0 NA NA NA NA
46I,47V,54M,84V,90M 26 2 40.0 1 62.0 2 43.0 1 400.0 2 68.0 2 87.0 2 106.0 2 31.0
46L,48V,54V,82A,84V 25 4 47.0 4 260.0 4 34.0 4 22.0 4 85.0 4 106.0 4 3.0 1 5.0
46I,82T,84V 25 8 3.9 8 2.5 7 7.2 8 3.1 3 19.0 6 8.7 2 2.5 2 1.6
54V,82S 25 1 15.0 1 4.0 1 17.0 1 0.9 1 17.0 1 19.0 1 1.1 NA NA
46I,76V,90M 25 5 7.2 5 2.9 4 17.0 4 7.2 2 2.6 2 23.0 2 0.8 1 1.5
46I,54V,82F 24 1 19.0 1 0.1 1 1.7 1 5.8 NA NA NA NA NA NA NA NA
30N,46I,90M 24 1 121.0 1 15.0 1 6.0 1 2.5 1 6.6 1 2.4 NA NA NA NA
32I,46I,47V,54L,90M 24 1 74.0 1 70.0 1 11.0 1 89.0 1 89.0 1 71.0 1 1.2 1 48.0
54M,84V,90M 24 2 20.0 2 48.0 2 29.0 2 30.0 2 38.0 2 23.0 2 1.2 2 7.2
46L,48V,54V,82A,90M 24 1 44.0 1 40.0 1 6.9 1 39.0 NA NA NA NA NA NA NA NA
48V,82A 24 3 7.5 3 6.5 3 6.6 3 2.9 NA NA NA NA NA NA NA NA
54V,82T,84V 24 3 21.0 3 73.0 3 30.0 3 6.7 2 24.0 3 26.0 2 26.0 1 1.7
48V 23 1 0.8 1 5.3 1 1.0 1 1.0 1 2.6 1 0.8 1 0.4 1 0.4
46L,48V,54T,82A 23 3 139.0 2 467.0 3 171.0 3 8.7 3 66.0 NA NA NA NA NA NA
54A,82A 23 1 184.0 1 135.0 1 106.0 1 19.0 1 133.0 1 136.0 1 5.1 NA NA
46I,50L,82A,90M 22 1 6.0 1 2.5 1 4.8 1 3.5 1 49.0 1 2.1 1 1.0 1 0.8
82A,84V 22 1 13.0 1 31.0 1 6.8 1 43.0 1 29.0 NA NA NA NA NA NA
54A,82A,90M 22 3 136.0 3 66.0 3 143.0 3 9.3 1 242.0 3 108.0 1 2.7 NA NA
46I,54V,76V,82F,90M 22 2 66.0 2 2.3 2 335.0 2 24.0 2 2.5 2 255.0 2 1.1 NA NA
32I,54L,84V,90M 22 6 55.0 6 80.0 6 21.0 6 167.0 6 261.0 6 62.0 6 5.9 5 334.0
46I,54V,82C,90M 21 1 54.0 1 27.0 1 20.0 1 7.1 1 29.0 1 144.0 1 5.2 1 2.4
46I,54L,82A,90M 21 1 250.0 1 50.0 1 109.0 1 119.0 1 311.0 1 292.0 1 2.8 NA NA
48V,82A,90M 21 1 25.0 1 105.0 1 22.0 1 2.1 1 7.8 NA NA NA NA NA NA
32I,46L,82A,90M 21 1 22.0 1 4.9 1 16.0 1 4.5 1 14.0 1 6.4 NA NA NA NA
46I,82T,84V,90M 21 3 23.0 3 38.0 3 33.0 2 3.4 2 16.0 NA NA NA NA NA NA
30N,54L,90M 20 6 156.0 6 22.0 6 4.5 6 11.0 4 36.0 3 14.0 2 0.8 1 16.0
48M,54V,82A,90M 20 2 372.0 2 675.0 2 290.0 2 61.0 1 141.0 2 250.0 NA NA NA NA
46I,50V,54V,90M 20 1 93.0 1 1000.0 1 5.0 1 31.0 1 47.0 1 94.0 1 0.5 1 30.0
46I,50L,90M 19 1 8.9 1 2.6 1 4.3 1 1.9 1 78.0 1 1.0 1 0.5 1 0.6
30N,54V,82A,90M 19 2 355.0 2 110.0 2 77.0 2 10.0 2 105.0 2 98.0 2 1.7 1 1.6
46I,47V,54V,84V 19 4 23.0 4 60.0 4 16.0 4 41.0 2 39.0 4 80.0 2 17.0 NA NA
46L,88S 19 5 12.0 5 1.2 5 2.9 5 0.1 NA NA NA NA NA NA NA NA
32I,46I,47A 19 2 49.0 2 0.8 2 26.0 2 45.0 1 8.8 2 165.0 2 3.1 1 9.3
46I,54A,82A,90M 18 1 89.0 1 59.0 1 150.0 1 5.6 1 65.0 1 75.0 NA NA NA NA
46L,48V,54S,82A 18 1 99.0 1 293.0 1 117.0 1 14.0 1 57.0 1 105.0 1 1.4 NA NA
46I,54L,76V,84V 18 2 2.9 2 2.0 2 6.1 2 40.0 2 2.0 2 82.0 2 0.6 1 17.0
46I,50V,90M 18 1 19.0 1 21.0 1 9.1 1 56.0 1 2.5 1 39.0 NA NA NA NA
46I,48V,54T,82A 18 2 106.0 2 217.0 2 80.0 2 6.7 1 34.0 1 69.0 1 0.4 NA NA
30N,54V,82A 17 2 335.0 2 23.0 2 26.0 2 26.0 2 26.0 2 73.0 2 3.3 2 3.5
32I,46I,47V,54L,84V 17 3 5.8 3 5.1 3 5.8 3 132.0 3 17.0 3 232.0 3 1.8 3 103.0
46I,76V,82A 17 1 3.8 1 0.4 1 18.0 1 4.3 1 1.2 1 23.0 NA NA NA NA
32I,90M 17 3 10.0 3 2.8 3 3.1 3 3.1 3 5.1 3 1.2 3 1.1 3 1.1
46I,54V,76V,82T 17 3 31.0 3 8.2 3 500.0 3 17.0 3 7.7 3 500.0 3 1.4 3 3.6
46L,54L,84V,90M 17 2 51.0 2 93.0 2 11.0 2 88.0 1 38.0 2 29.0 1 7.6 1 52.0
46L,54V,82T,90M 17 4 56.0 4 71.0 4 40.0 4 14.0 4 60.0 4 71.0 4 16.0 3 3.3
46L,54V,82T 17 3 13.0 3 5.0 3 21.0 3 11.0 3 10.0 3 25.0 2 12.0 1 2.7
46I,54M,90M 16 2 41.0 2 65.0 2 16.0 2 48.0 1 75.0 2 28.0 1 3.4 1 27.0
50V,54V,82A 16 1 19.0 1 337.0 1 19.0 1 43.0 1 12.0 1 106.0 1 0.3 NA NA
46I,82F 16 1 7.4 1 0.2 1 2.3 1 2.2 1 4.5 NA NA NA NA NA NA
46L,54L,82A,84V,90M 16 1 136.0 1 79.0 1 37.0 1 122.0 1 288.0 1 146.0 1 8.7 1 256.0
54L,82A,84V,90M 15 1 60.0 1 158.0 1 24.0 1 90.0 1 180.0 1 80.0 1 17.0 1 22.0
48A,54V,82A 15 1 64.0 1 67.0 1 38.0 1 11.0 1 185.0 1 132.0 1 5.4 1 1.7
32I,47V,54M,84V,90M 15 1 49.0 1 39.0 1 80.0 1 184.0 1 132.0 1 185.0 1 21.0 1 434.0
32I,46I,84V,90M 15 4 150.0 4 156.0 4 52.0 3 200.0 3 200.0 4 66.0 3 9.6 1 36.0
46I,54L,90M 15 1 34.0 1 47.0 1 25.0 1 13.0 1 33.0 1 20.0 1 0.8 1 5.4
30N,50L 14 1 6.0 1 0.1 1 0.1 1 22.0 NA NA NA NA NA NA NA NA
48V,50V,54S,82A 14 1 202.0 1 293.0 1 224.0 1 112.0 1 112.0 1 324.0 1 0.9 NA NA
32I,46I,47A,82A 14 2 28.0 2 0.6 2 50.0 2 55.0 2 19.0 2 500.0 2 6.3 2 13.0
46I,88T 14 1 11.0 1 1.1 1 6.0 1 4.0 NA NA NA NA NA NA NA NA
46L,54L,82A 14 2 11.0 2 2.4 2 7.2 2 12.0 1 14.0 2 15.0 1 2.1 NA NA
46L,54V,82T,84V 14 1 25.0 1 37.0 1 52.0 1 19.0 1 53.0 1 59.0 1 200.0 1 5.6
30N,84V,90M 14 4 600.0 4 700.0 4 19.0 4 29.0 4 98.0 4 29.0 1 3.1 1 7.2
50L,82M 13 1 0.9 1 0.3 1 1.4 1 8.0 1 28.0 1 1.9 1 3.5 1 1.0
48V,54V,82A,84V,90M 13 1 113.0 1 1000.0 1 102.0 1 30.0 1 122.0 NA NA NA NA NA NA
82F,90M 13 1 22.0 1 1.3 1 15.0 1 5.7 1 6.1 1 12.0 1 1.7 NA NA
32I,46I,47V,84V,90M 13 1 14.0 1 43.0 1 36.0 1 108.0 1 206.0 1 176.0 1 24.0 1 94.0
46L,54M,82A,90M 12 2 61.0 2 31.0 2 61.0 2 65.0 2 74.0 2 98.0 2 3.0 1 3.5
84C 12 6 67.0 6 37.0 6 2.7 6 7.4 3 5.0 4 2.2 NA NA NA NA
46I,76V,82F 12 1 6.5 1 0.5 1 21.0 1 27.0 1 0.6 1 54.0 NA NA NA NA
32I,46L,54L,84V,90M 12 5 74.0 5 36.0 5 18.0 5 186.0 5 117.0 5 87.0 5 14.0 5 239.0
82L,90M 12 1 2.6 1 1.2 1 1.4 1 1.2 NA NA NA NA NA NA NA NA
46L,54M,84V,90M 12 3 55.0 3 66.0 3 22.0 3 148.0 2 395.0 3 70.0 2 11.0 2 314.0
46L,82A,84V,90M 12 2 20.0 2 43.0 2 15.0 2 18.0 2 49.0 2 31.0 1 14.0 1 15.0
32I,47V,90M 12 1 78.0 1 51.0 1 67.0 1 400.0 1 157.0 1 500.0 1 800.0 1 200.0
46I,48V,54S,82A 11 1 23.0 1 1000.0 1 115.0 1 11.0 1 110.0 1 139.0 1 2.6 1 2.0
32I,46I,54L,84V,90M 11 2 43.0 2 50.0 2 22.0 2 142.0 2 258.0 2 86.0 2 3.5 2 204.0
32I,54L,84V 11 1 8.0 1 2.3 1 3.9 1 57.0 1 17.0 1 15.0 1 4.6 1 35.0
46I,50L,54V,82A,90M 11 2 9.7 2 3.1 2 8.2 2 5.0 2 142.0 2 13.0 2 1.1 1 1.7
46I,82A,84V,90M 11 1 38.0 1 99.0 1 20.0 1 26.0 1 122.0 1 48.0 1 6.0 NA NA
32I,47A,90M 11 1 5.3 1 2.0 1 13.0 1 43.0 1 5.1 1 112.0 1 1.4 1 6.8
46I,54M,84V 11 2 29.0 2 21.0 2 21.0 2 117.0 2 49.0 2 49.0 2 2.0 2 28.0
32I,46I,47V,84V 11 2 31.0 2 6.0 2 17.0 2 41.0 2 40.0 2 77.0 1 16.0 1 25.0
46I,50V,76V 11 5 1.3 5 0.9 1 1.0 5 6.0 5 1.0 5 10.0 1 0.8 1 1.0
32I,47V,82A 10 1 2.1 1 0.2 1 3.3 1 2.1 1 2.7 1 0.4 1 0.5 NA NA
30N,82A 10 1 45.0 1 2.3 1 1.8 1 1.2 1 2.5 1 1.2 NA NA NA NA
46I,84A 10 6 600.0 6 628.0 6 65.0 6 32.0 3 52.0 5 14.0 NA NA NA NA
46I,50L,54V,82A 10 1 8.3 1 1.6 1 4.2 1 2.6 1 76.0 1 3.6 NA NA NA NA
46I,47A,84V,90M 10 1 92.0 1 25.0 1 73.0 1 129.0 1 37.0 1 500.0 1 10.0 1 35.0
46I,48V,50V,54T,82A 10 1 53.0 1 1000.0 1 160.0 1 130.0 1 49.0 1 500.0 1 1.7 1 54.0
32I,47V,54L,90M 10 1 32.0 1 15.0 1 19.0 1 43.0 1 67.0 NA NA NA NA NA NA
32I,46L,54V,82A,90M 10 2 198.0 2 211.0 2 119.0 2 40.0 2 191.0 2 102.0 2 4.9 NA NA
30N,46L,54V,90M 10 3 142.0 3 87.0 3 14.0 3 1.8 3 34.0 3 15.0 2 4.5 2 4.8
30N,84V 10 2 152.0 2 40.0 2 8.2 2 6.7 2 35.0 1 11.0 NA NA NA NA
32I,82A,90M 10 1 23.0 1 4.9 1 14.0 1 15.0 1 9.3 1 16.0 1 1.0 NA NA
32I,46I,54M,82A,90M 10 3 54.0 3 24.0 3 22.0 3 54.0 3 140.0 3 56.0 3 3.0 2 34.0
46I,48V,50V,54S,82A 10 4 113.0 3 1000.0 3 400.0 4 90.0 4 100.0 3 500.0 2 1.6 1 39.0
46L,48V,54T,82A,90M 9 1 600.0 1 1000.0 1 500.0 1 36.0 1 700.0 1 263.0 1 3.6 1 10.0
54V,76V,82A,90M 9 1 3.2 1 1.0 1 26.0 1 4.9 1 0.4 1 54.0 1 0.5 1 1.4
46I,82F,84V 9 1 204.0 1 79.0 1 54.0 1 172.0 1 256.0 NA NA NA NA NA NA
32I,46I,47V,54M,84V 9 1 26.0 1 14.0 1 19.0 1 126.0 1 56.0 1 130.0 1 4.3 NA NA
46L,54V,82C,90M 9 2 156.0 1 93.0 2 51.0 2 28.0 1 83.0 2 118.0 1 17.0 1 21.0
46L,54L,90M 9 1 22.0 1 15.0 1 4.4 1 25.0 1 13.0 1 8.0 1 1.3 1 12.0
32I,46I,54L,82A,90M 9 2 105.0 2 230.0 2 35.0 2 28.0 2 116.0 2 53.0 2 48.0 1 9.6
46L,48V,54V,82A,84V,90M 9 2 36.0 2 17.0 2 20.0 2 82.0 NA NA NA NA NA NA NA NA
32I,46I,47V,54V,84V,90M 9 1 97.0 1 62.0 1 59.0 1 140.0 1 347.0 1 500.0 1 200.0 1 114.0
46L,54V,82C,84V,90M 9 1 146.0 1 86.0 1 38.0 1 60.0 1 186.0 1 158.0 1 23.0 1 28.0
30N,54L,84V,90M 9 1 217.0 1 104.0 1 7.4 1 400.0 1 50.0 1 28.0 1 1.0 1 51.0
32I,46I,47V,54M,82T,90M 8 4 20.0 4 12.0 4 44.0 4 86.0 4 54.0 4 206.0 4 115.0 4 62.0
32I,46I,84V 8 1 9.3 1 3.5 1 9.9 1 24.0 1 52.0 1 14.0 1 2.7 1 22.0
46I,54L,84V 8 2 15.0 2 16.0 2 7.8 2 30.0 2 9.6 2 14.0 2 1.4 1 9.8
54V,82S,90M 8 3 32.0 3 9.4 3 16.0 3 2.8 1 11.0 3 51.0 1 4.1 NA NA
32I,54V,84V,90M 8 3 51.0 3 88.0 3 30.0 3 400.0 3 111.0 3 65.0 3 9.5 3 120.0
54M,84V 7 2 9.1 2 11.0 2 5.7 2 15.0 2 11.0 2 9.2 2 3.9 1 7.5
32I,47V,54M 7 1 1.6 1 0.7 1 2.6 1 17.0 1 1.8 1 9.7 1 1.6 1 9.6
82S 7 1 15.0 1 1.6 1 18.0 1 13.0 1 13.0 1 38.0 1 8.9 NA NA
46L,50V,82A 7 1 7.3 1 6.8 1 4.3 1 101.0 1 3.4 1 55.0 1 2.9 NA NA
50V,90M 7 1 10.0 1 8.4 1 2.9 1 13.0 1 2.0 1 12.0 NA NA NA NA
32I,46I,47V,50L,82A 7 1 2.7 1 0.4 1 3.9 1 6.8 1 123.0 1 11.0 1 4.3 1 1.7
30N,46L,54V,82A,90M 7 1 600.0 1 1000.0 1 57.0 1 8.0 1 51.0 1 97.0 1 1.1 1 1.1
46L,54L 7 1 3.6 1 2.4 1 2.9 1 5.1 1 3.0 1 5.0 1 0.8 1 2.4
30N,46I,54V 7 1 500.0 1 14.0 1 6.1 1 4.2 NA NA NA NA NA NA NA NA
30N,54L,84V 7 2 65.0 2 28.0 2 3.1 2 23.0 2 27.0 1 14.0 1 0.8 1 9.7
54L,82A,84V 7 1 13.0 1 17.0 1 3.3 1 24.0 1 17.0 1 12.0 1 2.1 1 6.1
32I,54V,82A,90M 7 1 124.0 1 26.0 1 9.3 1 7.7 1 42.0 1 21.0 1 5.8 1 3.1
32I,46I,47V,50V,54L 7 1 4.7 1 1.6 1 1.7 1 76.0 1 4.8 1 70.0 1 0.3 1 120.0
46I,54V,82F,84V 7 1 25.0 1 4.9 1 23.0 1 52.0 1 14.0 1 136.0 NA NA NA NA
46I,54V,88G,90M 7 3 200.0 3 99.0 2 224.0 3 31.0 2 281.0 3 206.0 2 15.0 1 7.7
46I,54V,76V,82A,84V 6 1 6.5 1 2.8 1 34.0 1 5.8 1 83.0 NA NA NA NA NA NA
54M,88S 6 1 16.0 1 15.0 1 15.0 1 1.4 1 61.0 1 3.4 1 1.0 1 1.9
32I,46I,47A,82A,90M 6 1 24.0 1 1.0 1 124.0 1 47.0 1 9.6 1 500.0 1 4.0 1 11.0
54L,82A 6 2 26.0 2 36.0 2 14.0 2 24.0 2 73.0 2 37.0 1 1.2 NA NA
46I,84V,88S 6 1 66.0 1 12.0 1 12.0 1 0.3 1 31.0 NA NA NA NA NA NA
46L,48V,54V,82S,90M 6 1 600.0 1 1000.0 1 500.0 1 15.0 1 700.0 1 500.0 1 4.8 1 3.1
30N,46I,54L,90M 6 1 550.0 1 45.0 1 6.8 1 28.0 NA NA NA NA NA NA NA NA
48V,54A,82A,90M 6 1 214.0 1 280.0 1 209.0 1 25.0 1 336.0 1 260.0 1 1.3 NA NA
54M,82A 6 3 7.7 3 1.9 3 5.0 3 22.0 3 4.0 3 11.0 1 1.1 1 1.2
46L,76V 6 1 1.1 1 0.8 1 4.4 1 9.6 1 0.6 1 9.8 1 0.4 NA NA
46I,47V,54V,82C,90M 6 1 67.0 1 400.0 1 9.4 1 40.0 1 58.0 1 116.0 1 29.0 NA NA
46I,54L,82A 5 1 46.0 1 10.0 1 28.0 1 47.0 1 118.0 1 62.0 1 0.9 1 8.2
32I,46I,47V,82T,90M 5 1 114.0 1 59.0 1 400.0 1 44.0 1 187.0 1 139.0 NA NA NA NA
32I,54L 5 1 7.9 1 2.5 1 4.3 1 6.4 1 17.0 1 2.6 1 0.2 1 2.9
46I,54V,76V,82M 5 1 9.9 1 1.3 1 56.0 1 27.0 1 2.5 1 94.0 1 0.8 1 9.1
46L,48M,54S,82A 5 2 50.0 2 256.0 2 66.0 2 18.0 2 54.0 2 91.0 1 6.1 NA NA
32I,54V,90M 5 3 58.0 3 83.0 3 24.0 3 18.0 3 79.0 2 19.0 2 2.6 2 11.0
46I,54V,84A 5 2 398.0 2 1000.0 2 148.0 2 37.0 2 477.0 2 63.0 NA NA NA NA
32I,46I,82A,84V 5 1 7.8 1 3.8 1 7.7 1 16.0 1 45.0 1 19.0 1 7.9 1 12.0
32I,84V,90M 5 1 26.0 1 13.0 1 13.0 1 20.0 1 61.0 1 10.0 1 2.1 1 13.0
46L,48S,54V,82A 5 2 87.0 2 209.0 2 17.0 2 3.1 2 102.0 NA NA NA NA NA NA
48V,50V,54T,82A 5 1 115.0 1 271.0 1 121.0 1 97.0 1 82.0 1 286.0 1 0.9 NA NA
46I,84V,88T,90M 5 1 55.0 1 92.0 1 49.0 1 2.6 1 36.0 1 2.8 NA NA NA NA
32I,54L,82A,84V,90M 4 1 37.0 1 38.0 1 42.0 1 155.0 1 170.0 1 168.0 1 23.0 1 612.0
32I,46I,54V,76V,82A 4 1 22.0 1 1.5 1 45.0 1 33.0 1 10.0 1 58.0 1 0.7 1 47.0
48V,50V,54A,82A,90M 4 2 441.0 2 633.0 2 367.0 2 76.0 2 134.0 2 407.0 2 0.8 1 14.0
30N,54V,84V 4 1 146.0 1 73.0 1 79.0 1 8.5 1 110.0 1 35.0 1 31.0 1 2.8
48V,50V,54V,82A,90M 4 1 42.0 1 97.0 1 122.0 1 36.0 1 28.0 1 185.0 1 0.1 1 16.0
46I,84C 4 1 86.0 1 68.0 1 6.4 1 12.0 1 2.9 NA NA NA NA NA NA
54V,82L 4 1 4.4 1 0.8 1 2.0 1 2.5 1 3.2 1 3.9 1 8.4 1 1.1
46L,54L,82T,90M 4 1 12.0 1 10.0 1 16.0 1 13.0 1 14.0 1 11.0 NA NA NA NA
46I,54V,82C,84V 4 1 24.0 1 26.0 1 27.0 1 23.0 1 21.0 1 79.0 1 5.6 1 8.1
46I,54S,82A,90M 4 1 156.0 1 280.0 1 176.0 1 72.0 1 101.0 1 148.0 1 10.0 NA NA
54M,82M,90M 4 1 13.0 1 2.0 1 8.6 1 21.0 1 13.0 1 5.9 1 3.0 NA NA
32I,46I,47V,54V,82T,90M 4 1 38.0 1 36.0 1 70.0 1 23.0 1 75.0 1 139.0 1 25.0 1 22.0
46L,76V,82A 4 1 13.0 1 2.9 1 41.0 1 50.0 1 3.2 1 100.0 1 0.8 1 12.0
48M,54V,82A,84V 4 1 132.0 1 1000.0 1 76.0 1 26.0 1 700.0 1 130.0 1 2.0 1 24.0
46I,48V,54T,82A,90M 4 1 118.0 1 267.0 1 160.0 1 6.9 1 105.0 1 49.0 1 1.0 NA NA
46L,54M,90M 4 1 32.0 1 3.7 1 8.3 1 9.9 NA NA NA NA NA NA NA NA
30N,46L,54L 4 1 133.0 1 21.0 1 1.4 1 8.2 1 35.0 1 4.6 1 0.2 1 1.7
32I,46I,54M,82A 4 1 29.0 1 1.8 1 20.0 1 31.0 NA NA NA NA NA NA NA NA
32I,46I,47V,50L 4 2 5.5 2 1.1 2 2.5 2 4.5 2 137.0 2 4.6 2 9.1 2 1.2
82F,84V 4 1 3.6 1 1.8 1 2.4 1 2.5 1 2.3 NA NA NA NA NA NA
32I,46I,47V,50V,54L,82A 4 2 14.0 2 12.0 2 20.0 2 170.0 2 9.9 2 186.0 2 0.8 2 496.0
32I,54L,82T,90M 4 1 26.0 1 13.0 1 21.0 1 17.0 1 26.0 1 14.0 1 0.4 NA NA
46I,47V,54V,82A,84V 3 1 8.2 1 5.9 1 20.0 1 44.0 1 7.3 1 134.0 1 6.6 1 12.0
46I,54V,82M 3 2 33.0 2 4.2 2 28.0 2 60.0 2 42.0 2 65.0 1 5.8 1 27.0
46I,47V,90M 3 2 50.0 2 13.0 2 6.2 2 47.0 2 34.0 2 9.1 2 27.0 2 23.0
48M,54S,82A 3 2 62.0 2 209.0 2 93.0 2 23.0 2 83.0 2 129.0 2 3.8 1 2.4
32I,46I,54M,84V,90M 3 1 32.0 1 20.0 1 54.0 1 200.0 1 204.0 1 98.0 1 4.2 1 117.0
48M,50V,54A,82A 3 1 89.0 1 200.0 1 200.0 1 46.0 1 200.0 1 200.0 1 1.3 1 33.0
46I,47V,76V,84A 3 1 210.0 1 69.0 1 152.0 1 141.0 1 21.0 1 104.0 NA NA NA NA
46I,88G 3 1 2.9 1 0.4 1 2.1 1 5.5 1 0.9 1 2.7 1 1.2 1 1.1
30N,32I,46I,47V,54L,84V,90M 3 1 36.0 1 7.5 1 491.0 NA NA NA NA NA NA NA NA NA NA
46I,76V,84A 3 2 332.0 2 145.0 2 219.0 2 137.0 2 54.0 NA NA NA NA NA NA
46I,50V,82T,90M 3 1 19.0 1 18.0 1 18.0 1 37.0 1 100.0 NA NA NA NA NA NA
30N,46I,54L,84V,90M 3 1 21.0 1 116.0 1 178.0 1 78.0 1 0.9 NA NA NA NA NA NA
46I,50V,54L,90M 3 1 26.0 1 30.0 1 7.9 1 46.0 1 5.4 1 17.0 1 0.2 1 14.0
32I,46I,82A,84V,90M 3 1 54.0 1 47.0 1 42.0 1 73.0 1 700.0 1 83.0 1 17.0 1 53.0
46I,54L,82T 3 1 8.9 1 2.9 1 5.4 1 1.8 1 12.0 1 0.7 1 0.8 NA NA
32I,54V,82T,90M 3 1 63.0 1 57.0 1 49.0 1 9.7 1 62.0 1 32.0 NA NA NA NA
46L,84C 3 3 395.0 3 92.0 3 11.0 3 20.0 3 3.1 NA NA NA NA NA NA
32I,46I,47V,54L,82T,90M 3 1 70.0 1 13.0 1 44.0 1 180.0 1 91.0 1 119.0 1 19.0 1 90.0
46I,47V,88G,90M 3 1 17.0 1 2.8 1 8.6 1 3.9 1 3.1 1 15.0 1 2.9 1 3.0
32I,46I,54M,90M 3 2 45.0 2 31.0 2 30.0 2 59.0 2 13.0 NA NA NA NA NA NA
46I,54V,76V,88G,90M 3 1 1.6 1 0.6 1 8.7 1 2.9 1 46.0 1 0.8 NA NA NA NA
46L,82L 3 1 1.3 1 0.5 1 0.7 1 2.1 1 0.8 NA NA NA NA NA NA
46L,54V,82T,84V,90M 2 2 86.0 2 503.0 2 116.0 2 82.0 2 355.0 2 110.0 2 103.0 1 0.9
46I,54M,84A 2 1 600.0 1 1000.0 1 400.0 1 400.0 1 700.0 1 59.0 NA NA NA NA
32I,46I,54V,76V,84V,90M 2 1 32.0 1 3.7 1 28.0 1 183.0 1 55.0 1 173.0 1 5.5 1 508.0
46I,54V,88S,90M 2 1 600.0 1 132.0 1 79.0 1 1.4 1 265.0 1 56.0 1 9.1 1 2.0
54L,76V,84V,90M 2 1 26.0 1 66.0 1 51.0 1 83.0 1 46.0 1 135.0 1 0.7 1 45.0
46I,50V,54L 2 1 9.4 1 8.4 1 0.9 1 29.0 1 2.2 1 9.2 1 0.3 NA NA
32I,46L,54L,82A,84V 2 1 37.0 1 7.7 1 13.0 1 42.0 1 86.0 1 49.0 1 2.5 1 46.0
48V,54T,82T 2 1 52.0 1 250.0 1 138.0 1 4.9 1 75.0 1 46.0 1 2.9 NA NA
46I,54V,76V,82A,88G,90M 2 1 8.5 1 0.4 1 6.8 1 6.6 1 79.0 NA NA NA NA NA NA
46L,54L,84C 2 1 70.0 1 115.0 1 5.5 1 30.0 1 9.1 1 2.3 NA NA NA NA
46I,54V,82L,90M 2 2 138.0 2 11.0 2 56.0 2 17.0 2 130.0 2 45.0 2 200.0 2 5.7
46I,54M,76V,82A 2 1 8.1 1 1.0 1 26.0 1 33.0 1 1.8 1 70.0 NA NA NA NA
32I,46I,47V,82C,90M 2 1 25.0 1 15.0 1 15.0 1 21.0 1 24.0 1 78.0 NA NA NA NA
54L,82F,90M 2 1 95.0 1 4.8 1 49.0 1 43.0 1 28.0 1 61.0 1 2.9 1 18.0
46L,48V,54L,82A,84V 2 1 19.0 1 81.0 1 9.4 1 25.0 1 22.0 1 28.0 1 1.3 1 12.0
48V,54T,82A,84V 2 2 69.0 2 1000.0 2 312.0 1 42.0 2 357.0 2 85.0 1 4.2 1 14.0
32I,46I,47V,54L,82C,90M 2 1 33.0 1 8.7 1 23.0 1 87.0 1 27.0 1 145.0 1 1.5 1 80.0
46I,54V,82A,88G 2 1 14.0 1 1.1 1 9.7 1 1.7 1 6.6 1 23.0 1 2.5 NA NA
32I,46L,47V,54M,84V,90M 2 1 600.0 1 86.0 1 177.0 1 400.0 1 700.0 1 500.0 1 800.0 1 200.0
48L,54V,82A,90M 2 1 47.0 1 293.0 1 50.0 1 7.1 1 143.0 1 116.0 1 1.2 NA NA
46L,50V,82A,90M 2 1 19.0 1 16.0 1 15.0 1 97.0 1 10.0 1 69.0 1 0.9 1 26.0
46I,47V,50V,54V,82A,90M 2 1 20.0 1 32.0 1 58.0 1 141.0 1 5.7 1 166.0 1 0.5 1 188.0
32I,46L,47V,54M,90M 2 1 44.0 1 18.0 1 43.0 1 56.0 1 46.0 1 70.0 1 9.5 NA NA
32I,46I,47V,54M,76V,84V 2 1 79.0 1 12.0 1 130.0 1 150.0 1 167.0 1 171.0 1 29.0 1 525.0
46L,48M,54M,82A,84V 2 2 7.2 2 79.0 2 8.2 2 47.0 2 24.0 2 41.0 2 4.5 2 13.0
46L,50V,82T,90M 2 2 5.8 2 11.0 2 12.0 2 106.0 2 5.2 2 105.0 2 2.7 2 128.0
32I,46I,47V,50L,82T,90M 2 1 8.3 1 1.3 1 13.0 1 2.2 1 161.0 1 8.0 1 4.5 1 0.7
32I,47V,54L,82L,90M 2 2 14.0 2 2.4 2 5.6 2 41.0 2 17.0 2 31.0 2 11.0 2 36.0
48V,50V,54A,82T 2 1 29.0 1 1000.0 1 97.0 1 6.1 1 17.0 1 118.0 1 0.6 1 2.2
46I,50V,82A,84V 2 2 2.6 2 3.9 2 7.8 2 179.0 2 3.0 2 121.0 2 12.0 2 284.0
30N,46I,54L,82A,90M 2 2 71.0 2 5.2 2 8.2 2 32.0 2 21.0 2 39.0 2 0.8 2 5.8

5.3 Supplementary Table S3. Cleaned Combination Mutations for INSTIs

insticombination_table <- read_xlsx(file.path(output_dir, "INSTI_combination_cleaned.xlsx"))
kable(insticombination_table, caption = "Supplementary Table S3: Cleaned Combination Mutations for INSTIs")
Supplementary Table S3: Cleaned Combination Mutations for INSTIs
MutPatterns NumSeqs RAL_n RAL_fold EVG_n EVG_fold DTG_n DTG_fold
155H 495 40 17.0 35 40.0 24 1.5
140S,148H 295 43 143.0 35 150.0 33 5.5
143R 140 25 87.0 21 8.0 11 1.1
92Q 86 26 4.8 25 40.0 11 1.4
263K 72 10 1.1 10 4.5 9 2.0
138K 62 7 0.9 7 0.9 5 0.8
143C 51 21 14.0 19 2.9 7 0.9
92Q,155H 50 8 139.0 5 150.0 4 3.0
148R 42 15 30.0 12 109.0 11 0.9
92G 38 4 1.6 4 13.0 3 1.0
140S,148R 34 6 147.0 3 150.0 4 5.1
66I 33 11 1.1 11 15.0 8 0.4
138A,140S,148H 32 3 188.0 3 164.0 3 7.4
138K,140S,148H 29 3 143.0 3 150.0 3 5.3
140A,148R 24 4 116.0 3 150.0 3 2.8
138K,148R 23 4 65.0 2 132.0 3 2.0
138K,147G,148R 21 2 34.0 2 165.0 NA NA
66A 19 3 0.9 3 7.6 3 0.3
147G 16 11 1.3 12 8.0 7 1.0
143H 12 15 4.1 15 2.5 3 0.9
143S 12 12 21.0 12 5.0 NA NA
148H 11 9 18.0 6 5.4 5 0.5
118R 11 7 13.0 8 6.8 7 11.0
138A 10 2 1.1 2 1.3 2 0.9
140C,148R 8 2 86.0 2 174.0 1 9.1
145S 8 2 0.7 2 28.0 2 0.3
151A 8 2 1.4 2 2.7 2 0.8
148R,155H 8 3 102.0 3 114.0 2 4.3
138K,140A,148K 8 1 143.0 1 150.0 1 63.0
140R 7 1 2.2 NA NA NA NA
121Y 7 6 9.4 6 27.0 5 1.1
143G 7 12 29.0 12 7.0 NA NA
138K,140A,148R 6 1 105.0 1 114.0 1 13.0
140S 6 4 1.6 4 5.0 2 0.8
146P 5 2 0.8 2 6.5 2 0.5
138T,140S,148H 5 1 119.0 NA NA NA NA
138K,140C,148R 5 1 143.0 1 150.0 1 8.6
140S,148N 4 2 0.6 2 3.6 2 0.6
138K,147G,155H 4 3 150.0 3 150.0 3 55.0
118R,138K 3 2 17.0 2 5.0 2 10.0
66I,155H 3 1 19.0 1 94.0 1 1.1
66K 3 3 8.0 3 40.0 3 1.7
66I,92Q 3 2 23.0 2 120.0 1 0.6
148K 2 8 37.0 6 82.0 5 0.8
151L 2 2 15.0 2 20.0 2 1.6
66I,148R 2 1 53.0 1 94.0 1 3.4
92Q,147G 2 3 6.4 3 160.0 NA NA

6 Conclusion

This supplementary analysis identifies key mutations associated with reduced susceptibility for NRTIs, PIs, and INSTIs.
Low-frequency mutations and incomplete fold data were excluded to ensure robustness.
The cleaned combination mutation datasets are included to support reproducibility.