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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 |
| 5tat |
0 |
58 |
52 |
B |
B |
12_BF |
Undecided |
| vpu |
91 |
324 |
95 |
B |
B |
B (Major agrees Nested with high confidence) |
| env |
241 |
2785 |
1588 |
B |
B |
B (Unambiguous Nested) |
Subtype Prediction for Associated Protein Sequences
| NCBI GI |
ACCESSION |
Gene |
Start |
Stop |
Length |
Major Subtype |
Nested Analysis |
Final Decision |
| 187947148 |
ACD41614 |
env |
33 |
847 |
551 |
B |
B |
B (Unambiguous Nested) |
| Detailed result for 5tat (major) |
Outlierness: 0.570926 (all), 1.47923 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
9.09147e-11 |
| A |
4.6854e-08 |
| B |
0.994383 |
| C |
6.67608e-11 |
| D |
0.000515942 |
| F |
4.57039e-07 |
| G |
3.38091e-08 |
| H |
1.75583e-42 |
| J |
3.98133e-09 |
| K |
0.00510058 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 40 / 659 at 10 Dimensional MDS |
Predicted
Objective 01_AE A B C D F G H K
01_AE 42 8 0 0 0 0 2 0 1
A 3 55 0 1 0 0 4 0 0
B 0 0 158 1 0 0 0 0 0
C 0 0 0 307 0 0 0 0 0
D 0 0 3 0 40 1 0 0 0
F 0 0 0 2 1 8 0 0 1
G 4 3 0 1 0 0 7 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: 1.75931 (all), 5.96181 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
0.00886191 |
| 07_BC |
4.20961e-37 |
| 08_BC |
7.0386e-15 |
| 12_BF |
0.693739 |
| 14_BG |
4.20504e-19 |
| 15_01B |
3.69482e-15 |
| B |
0.297399 |
|
| 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 vpu (major) |
Outlierness: 0.787834 (all), 0.95069 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
1.09358e-16 |
| A |
3.7302e-14 |
| B |
1 |
| C |
3.91097e-13 |
| D |
2.02822e-07 |
| F |
5.90743e-10 |
| G |
1.47791e-13 |
| H |
3.41501e-12 |
| J |
4.23313e-21 |
| K |
4.1084e-20 |
|
| 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: 1.12515 (all), 1.10797 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
5.94747e-06 |
| 08_BC |
8.46972e-23 |
| 12_BF |
0.0591079 |
| 14_BG |
1.61144e-28 |
| 15_01B |
1.07064e-16 |
| B |
0.940886 |
|
| 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: 0.994928 (all), 1.00898 (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: 1.01034 (all), 1.00973 (group) |
|
| Subtype |
Posterior Probability |
| 03_AB |
0.00144539 |
| 07_BC |
0 |
| 08_BC |
0 |
| 12_BF |
1.1466e-32 |
| 14_BG |
0.00110189 |
| 15_01B |
5.81016e-16 |
| B |
0.997453 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 17 / 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 8 2 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
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| Plot in the First 3 Principal Coordinates |
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