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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 |
| ltr |
73 |
153 |
59 |
|
B |
B |
B (Major agrees Nested with high confidence) |
| Detailed result for ltr (major) |
Outlierness: 0.499909 (all), 0.518477 (group) |
|
| Subtype |
Posterior Probability |
| 01_AE |
0.000000000000152873 |
| A |
0.0106638 |
| B |
0.952553 |
| C |
0.00145257 |
| D |
0.0335096 |
| F |
0.00182053 |
| G |
0.000000000000741021 |
| H |
0.0000000180743 |
| J |
9.97987e-23 |
| K |
0.0000000127271 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 36 / 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 20 1 1 2 0 1 0 0 0
B 1 1 55 1 3 1 0 0 0 0
C 0 2 1 69 0 1 0 1 0 1
D 1 0 7 3 27 0 0 0 0 0
F 0 0 3 0 1 4 0 0 0 0
G 0 0 0 0 0 0 9 0 0 0
H 0 0 0 1 0 0 0 2 0 0
J 0 0 0 0 0 0 0 0 2 0
K 0 0 0 2 0 0 0 0 0 0
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| Plot in the First 3 Principal Coordinates |
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| Detailed result for ltr (nested) |
Outlierness: 0.444206 (all), 0.450285 (group) |
|
| Subtype |
Posterior Probability |
| 02_AG |
0.000000014474 |
| 03_AB |
0.0000000036147 |
| 04_cpx |
3.40698e-18 |
| 05_DF |
0.0000062626 |
| 06_cpx |
0.00000000153535 |
| 07_BC |
0.00000257289 |
| 08_BC |
0.000000141001 |
| 09_cpx |
9.44178e-19 |
| 10_CD |
0.00000037373 |
| 11_cpx |
5.78467e-17 |
| 12_BF |
0.000046363 |
| 16_A2D |
0.000000000805885 |
| A |
0.0000903486 |
| B |
0.945099 |
| D |
0.0547552 |
|
| Cross-Validation of Discriminant Models |
| Miss-Classification Rate: 39 / 182 at 10 Dimensional MDS |
Predicted
Objective 02_AG 03_AB 04_cpx 06_cpx 07_BC 08_BC 10_CD 11_cpx 12_BF 16_A2D A B
02_AG 25 1 0 0 0 0 0 0 0 0 2 0
03_AB 0 2 0 0 0 0 0 0 0 0 0 0
04_cpx 0 0 0 1 0 0 0 1 0 0 0 0
05_DF 0 0 0 0 0 0 0 0 0 0 0 1
06_cpx 0 0 0 4 0 0 0 0 0 0 0 0
07_BC 0 0 0 0 2 0 0 0 0 0 0 0
08_BC 0 0 0 0 1 4 0 0 0 0 0 0
09_cpx 0 0 0 0 0 0 0 0 0 0 0 0
10_CD 0 0 0 1 0 0 0 0 0 0 0 0
11_cpx 0 0 0 0 0 0 0 4 0 0 0 0
12_BF 0 0 0 0 0 0 0 0 2 0 0 1
16_A2D 0 0 0 0 0 0 0 0 0 0 0 0
A 1 3 0 0 0 0 0 0 0 2 18 1
B 0 0 0 0 0 0 0 0 1 0 1 58
D 0 0 1 0 1 0 2 0 1 1 0 8
Predicted
Objective D
02_AG 0
03_AB 0
04_cpx 0
05_DF 1
06_cpx 0
07_BC 0
08_BC 0
09_cpx 0
10_CD 2
11_cpx 0
12_BF 0
16_A2D 0
A 0
B 2
D 24
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| Plot in the First 3 Principal Coordinates |
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