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Virus: HIV-1 / Sequence Type: Nucleotide
Sequence Description:
(Link to NCBI GenBank)
Multiple Substitution Correction Algorithm: Jukes-Cantor
All sites that include gaps were deleted.
Gene by Gene Subtype Prediction Summary
| Gene |
Start |
Stop |
Length |
LANL Subtype |
Major Subtype |
Nested Analysis |
Final Decision |
| gag |
335 |
1838 |
963 |
B |
B |
B |
B (Unambiguous Nested) |
| pol |
1630 |
4642 |
2703 |
B |
B |
B (Unambiguous Nested) |
| vif |
4586 |
5165 |
522 |
B |
B |
B (Unambiguous Nested) |
| vpr |
5104 |
5396 |
147 |
B |
B |
B (Unambiguous Nested) |
| 5tat |
5376 |
5587 |
185 |
B |
B |
B (Unambiguous Nested) |
| vpu |
5620 |
5856 |
95 |
B |
B |
B (Major agrees Nested with high confidence) |
| env |
5770 |
8341 |
1585 |
B |
B |
B (Unambiguous Nested) |
| nef |
8342 |
8963 |
246 |
B |
B |
B (Unambiguous Nested) |
| ltr |
8631 |
9181 |
256 |
B |
B |
B (Unambiguous Nested) |
Subtype Prediction for Associated Protein Sequences
| NCBI GI |
ACCESSION |
Gene |
Start |
Stop |
Length |
Major Subtype |
Nested Analysis |
Final Decision |
| 2801502 |
AAC82591 |
tat |
0 |
86 |
79 |
B |
B |
B (Unambiguous Nested) |
| Detailed result for gag (major) |
Outlierness: 0.587477 (all), 0.240383 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
0 |
| A |
0 |
| B |
1 |
| C |
0 |
| D |
2.09395e-20 |
| F |
7.00649e-44 |
| G |
0 |
| H |
6.0438e-42 |
| J |
9.52923e-29 |
| K |
3.68534e-36 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 10 / 1142 at 10 Dimensional MDS |
Predicted
Objective 01_AE A B C D F G H K
01_AE 72 0 0 0 0 0 0 0 0
A 0 129 0 1 0 0 1 2 0
B 0 0 262 0 1 2 0 0 0
C 0 0 0 552 0 0 0 1 0
D 0 0 0 0 76 0 0 0 0
F 0 0 0 0 0 14 0 0 1
G 0 0 0 0 0 0 21 0 0
H 0 0 0 0 0 0 0 3 0
J 0 0 0 0 0 0 0 0 0
K 0 0 0 0 0 0 0 0 3
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for gag (nested) |
Outlierness: 0.302629 (all), 0.322256 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
0 |
| 07_BC |
1.1911e-43 |
| 08_BC |
0 |
| 12_BF |
1.22953e-16 |
| 14_BG |
0 |
| 15_01B |
0 |
| B |
1 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 6 / 290 at 10 Dimensional MDS |
Predicted
Objective 07_BC 08_BC 12_BF 15_01B B
03_AB 0 0 0 0 0
07_BC 3 0 0 0 0
08_BC 0 5 0 0 0
12_BF 0 0 8 0 2
14_BG 0 0 0 0 0
15_01B 0 0 0 5 0
B 0 0 2 0 263
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for pol (major) |
Outlierness: 0.76993 (all), 0.691563 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
0 |
| A |
0 |
| B |
1 |
| C |
0 |
| D |
0 |
| F |
0 |
| G |
0 |
| H |
0 |
| J |
0 |
| K |
0 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 3 / 735 at 10 Dimensional MDS |
Predicted
Objective 01_AE A B C D F G H K
01_AE 57 0 0 0 0 0 0 0 0
A 0 58 0 1 0 0 0 0 0
B 0 0 168 0 0 0 0 0 0
C 0 0 0 371 0 0 0 0 0
D 0 0 0 0 46 0 0 0 0
F 0 0 0 0 0 11 0 0 1
G 0 0 0 0 0 0 16 0 0
H 0 0 0 0 0 0 0 3 0
J 0 0 0 0 0 0 0 0 0
K 0 0 0 0 0 0 0 0 2
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for pol (nested) |
Outlierness: 0.479785 (all), 0.616533 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
1.01537e-06 |
| 07_BC |
0 |
| 08_BC |
0 |
| 12_BF |
0 |
| 14_BG |
0 |
| 15_01B |
0 |
| B |
0.999999 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 4 / 184 at 10 Dimensional MDS |
Predicted
Objective 12_BF 15_01B B
03_AB 0 0 0
07_BC 0 0 0
08_BC 0 0 0
12_BF 9 0 0
14_BG 0 0 0
15_01B 0 3 0
B 0 0 168
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for vif (major) |
Outlierness: 0.694772 (all), 1 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
0 |
| A |
2.40829e-40 |
| B |
1 |
| C |
1.98984e-43 |
| D |
1.06884e-19 |
| F |
1.07454e-40 |
| G |
2.38353e-38 |
| H |
3.89e-18 |
| J |
4.02728e-21 |
| K |
3.14215e-23 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 13 / 945 at 10 Dimensional MDS |
Predicted
Objective 01_AE A B C D F G H J
01_AE 53 0 0 0 0 0 0 0 0
A 0 70 0 0 0 0 4 0 0
B 0 0 370 0 0 0 0 0 0
C 0 0 0 364 0 0 0 0 0
D 0 0 0 0 47 0 0 1 0
F 0 0 0 0 0 10 0 3 0
G 0 1 0 0 0 0 16 0 0
H 0 0 0 0 0 0 0 2 1
J 0 0 0 0 0 0 0 0 0
K 0 0 0 0 0 2 0 0 0
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for vif (nested) |
Outlierness: 0.394083 (all), 0.698542 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
4.62597e-06 |
| 12_BF |
4.48416e-44 |
| 14_BG |
5.87214e-39 |
| 15_01B |
0 |
| B |
0.999995 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 2 / 386 at 10 Dimensional MDS |
Predicted
Objective 03_AB 12_BF 14_BG 15_01B B
03_AB 0 0 0 0 0
12_BF 0 9 0 0 0
14_BG 0 0 3 0 0
15_01B 0 0 0 3 0
B 1 0 0 0 369
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for vpr (major) |
Outlierness: 0.521138 (all), 0.485467 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
2.98627e-12 |
| A |
3.14701e-15 |
| B |
1 |
| C |
1.38627e-14 |
| D |
1.98088e-07 |
| F |
6.53846e-09 |
| G |
1.68185e-14 |
| H |
1.21641e-10 |
| J |
5.80776e-09 |
| K |
1.33587e-13 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 7 / 810 at 10 Dimensional MDS |
Predicted
Objective 01_AE A B C D F G H K
01_AE 31 0 0 0 0 0 0 0 0
A 1 55 0 0 0 0 0 0 0
B 0 0 283 0 1 0 0 1 0
C 0 0 0 364 0 0 0 0 0
D 0 0 1 0 43 0 0 0 0
F 0 0 0 0 0 9 0 0 0
G 1 0 0 0 0 0 14 0 0
H 0 0 0 0 0 1 0 2 0
J 0 0 0 0 0 0 0 0 0
K 0 0 0 0 0 0 0 0 2
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for vpr (nested) |
Outlierness: 0.0919241 (all), 0.308525 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
0.000222091 |
| 07_BC |
1.58825e-12 |
| 08_BC |
6.56592e-28 |
| 12_BF |
1.6942e-07 |
| 14_BG |
1.68898e-15 |
| 15_01B |
1.29555e-25 |
| B |
0.999778 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 11 / 300 at 10 Dimensional MDS |
Predicted
Objective 03_AB 07_BC 12_BF 14_BG 15_01B B
03_AB 0 0 0 0 0 0
07_BC 0 0 0 0 0 0
08_BC 0 0 0 0 0 0
12_BF 0 0 6 0 0 2
14_BG 0 0 0 0 0 0
15_01B 0 0 0 2 1 0
B 1 1 1 0 0 282
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for 5tat (major) |
Outlierness: 0.718512 (all), 0.553831 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
5.53649e-30 |
| A |
1.15151e-22 |
| B |
1 |
| C |
8.91476e-31 |
| D |
1.66004e-13 |
| F |
4.12596e-23 |
| G |
6.72788e-24 |
| H |
2.92868e-33 |
| J |
2.18201e-19 |
| K |
5.32602e-24 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 12 / 659 at 10 Dimensional MDS |
Predicted
Objective 01_AE A B C D F G H J K
01_AE 52 1 0 0 0 0 0 0 0 0
A 2 58 1 0 0 0 2 0 0 0
B 0 0 159 0 0 0 0 0 0 0
C 0 0 0 307 0 0 0 0 0 0
D 0 0 0 0 44 0 0 0 0 0
F 0 0 0 0 0 10 0 0 0 2
G 1 0 0 0 0 0 14 0 0 0
H 0 0 0 0 0 0 0 3 0 0
J 0 0 0 0 0 0 0 0 0 0
K 0 1 0 0 0 0 0 0 1 0
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for 5tat (nested) |
Outlierness: 0.646354 (all), 0.647002 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
0.0012809 |
| 07_BC |
2.57355e-15 |
| 08_BC |
3.07213e-24 |
| 12_BF |
3.7802e-09 |
| 14_BG |
1.52551e-19 |
| 15_01B |
9.98448e-27 |
| B |
0.998719 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 6 / 176 at 10 Dimensional MDS |
Predicted
Objective 12_BF 14_BG 15_01B B
03_AB 0 0 0 0
07_BC 0 0 0 0
08_BC 0 0 0 0
12_BF 7 0 0 3
14_BG 0 2 0 0
15_01B 0 0 2 0
B 0 0 0 159
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for vpu (major) |
Outlierness: 0.538347 (all), 0.664569 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
6.58929e-12 |
| A |
4.85637e-12 |
| B |
1 |
| C |
1.49351e-11 |
| D |
3.54829e-07 |
| F |
3.96918e-08 |
| G |
3.89067e-13 |
| H |
3.50756e-12 |
| J |
1.25929e-21 |
| K |
6.75856e-23 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 13 / 932 at 10 Dimensional MDS |
Predicted
Objective 01_AE A B C D F G H J
01_AE 44 2 0 0 0 0 0 0 0
A 3 64 1 0 0 0 0 2 0
B 0 0 321 0 0 0 0 0 0
C 0 0 0 397 0 0 0 0 0
D 0 0 0 0 54 0 0 0 0
F 0 0 0 0 0 12 0 0 0
G 0 0 0 0 0 0 22 0 0
H 0 3 0 0 0 0 0 3 0
J 0 0 0 0 0 0 0 0 2
K 0 0 0 0 0 1 1 0 0
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for vpu (nested) |
Outlierness: 0.814524 (all), 0.820469 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
0.00207889 |
| 08_BC |
3.92973e-18 |
| 12_BF |
0.0114234 |
| 14_BG |
1.81477e-34 |
| 15_01B |
2.57778e-13 |
| B |
0.986498 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 15 / 340 at 10 Dimensional MDS |
Predicted
Objective 12_BF 14_BG 15_01B B
03_AB 0 0 0 0
08_BC 0 0 0 0
12_BF 0 0 0 12
14_BG 0 3 0 0
15_01B 0 0 2 0
B 1 0 0 320
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for env (major) |
Outlierness: 0.818233 (all), 0.52192 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
0 |
| A |
0 |
| B |
1 |
| C |
0 |
| D |
0 |
| F |
0 |
| G |
0 |
| H |
0 |
| J |
0 |
| K |
0 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 2 / 1175 at 10 Dimensional MDS |
Predicted
Objective 01_AE A B C D F G H K
01_AE 70 0 0 0 0 0 0 0 0
A 0 82 0 0 0 0 0 0 0
B 0 0 454 0 0 0 0 0 0
C 0 0 0 464 0 0 0 0 0
D 0 0 0 0 60 0 0 0 0
F 0 0 0 0 0 15 0 0 1
G 0 0 0 0 0 0 23 0 0
H 0 0 0 0 0 0 0 3 0
J 0 0 0 0 0 0 0 0 0
K 0 0 0 0 0 0 0 0 2
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for env (nested) |
Outlierness: 0.825984 (all), 0.869246 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
0.000384498 |
| 07_BC |
0 |
| 08_BC |
0 |
| 12_BF |
9.54316e-39 |
| 14_BG |
2.1796e-11 |
| 15_01B |
4.81477e-13 |
| B |
0.999615 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 18 / 484 at 10 Dimensional MDS |
Predicted
Objective 07_BC 08_BC 12_BF 14_BG 15_01B B
03_AB 0 0 0 0 0 0
07_BC 7 3 0 0 0 0
08_BC 2 0 0 0 0 0
12_BF 0 0 8 0 0 2
14_BG 0 0 0 3 0 0
15_01B 0 0 0 0 4 0
B 0 0 0 0 10 444
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for nef (major) |
Outlierness: 0.7837 (all), 0.664416 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
0 |
| A |
3.6846e-31 |
| B |
1 |
| C |
1.01023e-34 |
| D |
1.71607e-12 |
| F |
7.68406e-24 |
| G |
0 |
| H |
5.27786e-32 |
| J |
8.40779e-44 |
| K |
8.03746e-28 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 6 / 1559 at 10 Dimensional MDS |
Predicted
Objective 01_AE A B C D F G H J K
01_AE 47 0 0 0 0 0 0 0 0 0
A 0 108 0 0 0 0 0 0 1 0
B 0 0 766 0 0 0 0 0 0 0
C 1 0 0 496 0 0 0 0 0 0
D 0 0 0 0 80 0 0 0 0 0
F 0 0 0 0 0 11 0 1 0 1
G 0 0 0 0 0 0 35 0 1 0
H 0 0 0 0 0 0 1 6 0 0
J 0 0 0 0 0 0 0 0 2 0
K 0 0 0 0 0 0 0 0 0 2
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for nef (nested) |
Outlierness: 0.625197 (all), 0.592366 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
0 |
| 07_BC |
1.79407e-28 |
| 08_BC |
9.55262e-40 |
| 12_BF |
9.77753e-16 |
| 14_BG |
0 |
| 15_01B |
0 |
| B |
1 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 6 / 795 at 10 Dimensional MDS |
Predicted
Objective 12_BF 14_BG 15_01B B
03_AB 0 0 0 0
07_BC 0 0 0 0
08_BC 0 0 0 0
12_BF 5 0 0 3
14_BG 0 14 0 0
15_01B 0 0 4 0
B 0 0 0 766
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for ltr (major) |
Outlierness: 0.811112 (all), 0.517433 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
1.37327e-42 |
| A |
3.52772e-23 |
| B |
1 |
| C |
5.21145e-27 |
| D |
1.61024e-16 |
| F |
5.21205e-28 |
| G |
9.38974e-39 |
| H |
1.84593e-19 |
| J |
7.76636e-38 |
| K |
5.77847e-26 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 3 / 276 at 10 Dimensional MDS |
Predicted
Objective 01_AE A B C D F G H J K
01_AE 52 0 0 0 0 0 0 0 0 0
A 0 24 0 0 0 0 1 0 0 0
B 0 0 62 0 0 0 0 0 0 0
C 0 0 0 74 0 0 0 0 0 1
D 0 0 0 0 38 0 0 0 0 0
F 0 0 0 0 0 8 0 0 0 0
G 0 0 0 0 0 0 9 0 0 0
H 0 1 0 0 0 0 0 2 0 0
J 0 0 0 0 0 0 0 0 2 0
K 0 0 0 0 0 0 0 0 0 2
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for ltr (nested) |
Outlierness: 0.535779 (all), 0.491409 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
1.26117e-44 |
| 07_BC |
1.27518e-43 |
| 08_BC |
2.8026e-44 |
| 12_BF |
9.34513e-38 |
| B |
1 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 3 / 74 at 10 Dimensional MDS |
Predicted
Objective 03_AB 07_BC 08_BC 12_BF B
03_AB 2 0 0 0 0
07_BC 0 0 2 0 0
08_BC 0 1 4 0 0
12_BF 0 0 0 3 0
B 0 0 0 0 62
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
|