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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 |
430 |
1670 |
842 |
? |
B |
B |
B (Unambiguous Nested) |
| pol |
1462 |
4473 |
2702 |
B |
B |
Undecided |
| vif |
4417 |
4995 |
521 |
B |
B |
Undecided |
| vpr |
4934 |
5100 |
103 |
B |
B |
B (Unambiguous Nested) |
| 5rev |
5343 |
5415 |
59 |
B |
B |
B (Major agrees Nested with high confidence) |
| 5tat |
5343 |
5415 |
66 |
B |
B |
B (Major agrees Nested with high confidence) |
| env |
6730 |
8058 |
829 |
B |
B |
Undecided |
| Detailed result for gag (major) |
Outlierness: 1.24817 (all), 2.07532 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
0 |
| A |
0 |
| B |
1 |
| C |
0 |
| D |
4.82612e-34 |
| F |
0 |
| G |
0 |
| H |
0 |
| J |
0 |
| K |
0 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 13 / 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 0 128 0 1 0 0 1 3 0
B 0 0 262 0 1 2 0 0 0
C 0 0 0 551 0 0 0 1 1
D 0 0 0 0 76 0 0 0 0
F 0 0 0 0 0 13 0 0 2
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: 1.76209 (all), 1.79847 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
0 |
| 07_BC |
0 |
| 08_BC |
0 |
| 12_BF |
2.29874e-31 |
| 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: 3.74056 (all), 18.7327 (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: 4 / 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 10 0 0 2
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: 15.8865 (all), 17.9529 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
0 |
| 07_BC |
0 |
| 08_BC |
0 |
| 12_BF |
0 |
| 14_BG |
0 |
| 15_01B |
0 |
| B |
1 |
|
| 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: 3.11642 (all), 5.08857 (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: 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 71 0 0 0 0 3 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 2 0 0 0 0 15 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: 3.06724 (all), 3.10136 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
0.000000000543467 |
| 12_BF |
0 |
| 14_BG |
0 |
| 15_01B |
0 |
| B |
1 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 1 / 386 at 10 Dimensional MDS |
Predicted
Objective 12_BF 14_BG 15_01B B
03_AB 0 0 0 0
12_BF 9 0 0 0
14_BG 0 3 0 0
15_01B 0 0 3 0
B 0 0 0 370
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for vpr (major) |
Outlierness: 1.01524 (all), 0.962563 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
0.00000000000000677734 |
| A |
3.86178e-23 |
| B |
0.999982 |
| C |
0.00000000000000462337 |
| D |
0.0000178581 |
| F |
0.00000000000364305 |
| G |
5.47534e-18 |
| H |
0.00000000000021508 |
| J |
5.36243e-17 |
| K |
2.95447e-16 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 19 / 810 at 10 Dimensional MDS |
Predicted
Objective 01_AE A B C D F G H K
01_AE 29 0 0 0 0 0 2 0 0
A 1 54 0 0 0 1 0 0 0
B 0 0 281 0 3 0 0 1 0
C 0 0 0 364 0 0 0 0 0
D 0 0 5 0 39 0 0 0 0
F 0 0 0 0 0 9 0 0 0
G 4 0 0 0 0 0 11 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: 0.833512 (all), 0.829614 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
0.0000648708 |
| 07_BC |
1.64341e-16 |
| 08_BC |
1.80591e-19 |
| 12_BF |
0.00000000196877 |
| 14_BG |
1.98254e-25 |
| 15_01B |
2.81827e-29 |
| B |
0.999935 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 13 / 300 at 10 Dimensional MDS |
Predicted
Objective 03_AB 12_BF 14_BG 15_01B B
03_AB 0 0 0 0 0
07_BC 0 0 0 0 0
08_BC 0 0 0 0 0
12_BF 0 6 0 0 2
14_BG 0 0 0 0 0
15_01B 0 0 2 1 0
B 3 2 0 0 280
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for 5rev (major) |
Outlierness: 1.38834 (all), 1.79705 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
1.04468e-22 |
| A |
0.000000000000210767 |
| B |
0.999999 |
| C |
0.0000000000181385 |
| D |
0.00000000185947 |
| F |
0.00000000329012 |
| G |
7.85368e-16 |
| H |
4.64726e-27 |
| J |
0.00000000000000150483 |
| K |
0.000000739247 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 58 / 703 at 10 Dimensional MDS |
Predicted
Objective 01_AE A B C D F G H J K
01_AE 48 3 0 1 0 0 6 0 0 0
A 4 47 0 8 0 0 2 0 0 0
B 0 0 150 1 2 1 0 0 0 0
C 0 4 0 345 0 1 0 0 0 0
D 0 1 4 0 40 1 0 0 0 0
F 0 1 0 3 1 6 0 0 0 1
G 3 5 0 1 0 0 7 0 0 0
H 0 1 0 0 0 0 0 2 0 0
J 0 0 0 0 0 0 0 0 0 0
K 0 0 0 0 0 1 0 0 1 0
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for 5rev (nested) |
Outlierness: 2.03322 (all), 2.04757 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
0.0079766 |
| 07_BC |
8.03354e-32 |
| 08_BC |
1.40086e-18 |
| 12_BF |
0.000136291 |
| 14_BG |
1.72077e-20 |
| 15_01B |
3.37243e-21 |
| B |
0.991887 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 16 / 173 at 10 Dimensional MDS |
Predicted
Objective 08_BC 12_BF 15_01B B
03_AB 0 0 0 0
07_BC 0 0 0 0
08_BC 2 0 0 0
12_BF 0 4 0 5
14_BG 0 0 2 0
15_01B 0 0 4 0
B 1 6 0 147
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for 5tat (major) |
Outlierness: 0.699806 (all), 1.42463 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
1.51479e-20 |
| A |
0.00000000000000193544 |
| B |
1 |
| C |
0.00000000000248018 |
| D |
0.0000000044592 |
| F |
0.000000000000824635 |
| G |
9.92327e-17 |
| H |
2.89598e-39 |
| J |
0.00000000000000269531 |
| K |
0.0000000000352293 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 41 / 659 at 10 Dimensional MDS |
Predicted
Objective 01_AE A B C D F G H K
01_AE 43 7 0 0 0 0 2 0 1
A 4 55 0 1 0 0 3 0 0
B 0 0 159 0 0 0 0 0 0
C 0 0 0 307 0 0 0 0 0
D 0 0 3 0 41 0 0 0 0
F 0 0 0 2 1 8 0 0 1
G 5 5 0 1 0 1 3 0 0
H 0 1 0 0 0 0 0 2 0
J 0 0 0 0 0 0 0 0 0
K 0 0 0 0 1 1 0 0 0
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for 5tat (nested) |
Outlierness: 1.97429 (all), 1.9851 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
0.0333939 |
| 07_BC |
2.2262e-38 |
| 08_BC |
2.37956e-17 |
| 12_BF |
0.000179475 |
| 14_BG |
8.18634e-32 |
| 15_01B |
1.76993e-24 |
| B |
0.966427 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 18 / 176 at 10 Dimensional MDS |
Predicted
Objective 03_AB 12_BF 14_BG 15_01B B
03_AB 0 0 0 0 0
07_BC 0 0 0 0 0
08_BC 0 0 0 0 0
12_BF 0 4 0 0 6
14_BG 0 0 1 1 0
15_01B 0 0 0 2 0
B 1 7 0 0 151
|
|
|
|
| Plot in the First 3 Principal Coordinates |
|
| Detailed result for env (major) |
Outlierness: 1.20159 (all), 2.28789 (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: 2.18357 (all), 2.23158 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
0.00996735 |
| 07_BC |
0 |
| 08_BC |
0 |
| 12_BF |
2.29751e-32 |
| 14_BG |
0.00000000000782032 |
| 15_01B |
1.24029e-17 |
| B |
0.990033 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 10 / 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 10 0 0 0 0 0
08_BC 0 2 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 7 447
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|
|
| Plot in the First 3 Principal Coordinates |
|
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