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Retrieval from the Database of Pre-calcuated Genotyping/Subtyping Results

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 829 2332 963 B B B B (Unambiguous Nested)
pol 2124 5136 2703 B B B (Unambiguous Nested)
vif 5080 5659 522 B B B (Unambiguous Nested)
vpr 5598 5890 147 B B B (Unambiguous Nested)
5tat 5870 6081 185 B B B (Unambiguous Nested)
vpu 6111 6347 95 B B B (Major agrees Nested with high confidence)
env 6261 8817 1587 B B B (Unambiguous Nested)
nef 8818 9439 246 B B B (Unambiguous Nested)
ltr 9107 9777 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
60193 CAA77621 gag 35 500 337 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.646001 (all), 0.744706 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 9.59313e-25
F 0
G 0
H 1.33123e-43
J 8.29362e-29
K 4.85299e-39

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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 0.533776 (all), 0.46282 (group)
Subtype Posterior Probability
03_AB 0
07_BC 0
08_BC 0
12_BF 2.81059e-17
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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (major) Outlierness: 0.773324 (all), 0.747465 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 2.68209e-42
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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 0.529705 (all), 0.628653 (group)
Subtype Posterior Probability
03_AB 0.000900907
07_BC 0
08_BC 0
12_BF 0
14_BG 0
15_01B 0
B 0.999099

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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vif (major) Outlierness: 0.789579 (all), 0.788517 (group)
Subtype Posterior Probability
01_AE 0
A 0
B 1
C 0
D 2.65331e-21
F 0
G 0
H 1.54839e-23
J 1.89354e-29
K 1.18723e-27

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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vif (nested) Outlierness: 0.751352 (all), 0.759085 (group)
Subtype Posterior Probability
03_AB 0.00198994
12_BF 0
14_BG 0
15_01B 0
B 0.99801

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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpr (major) Outlierness: 0.516608 (all), 0.330152 (group)
Subtype Posterior Probability
01_AE 0.000000000000056665
A 2.76494e-17
B 0.999999
C 0.0000000000000366735
D 0.000000572542
F 0.000000000480862
G 3.02354e-16
H 0.00000000000286402
J 0.000000000308779
K 0.00000000000000708374

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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpr (nested) Outlierness: 0.237209 (all), 0.247105 (group)
Subtype Posterior Probability
03_AB 0.000450034
07_BC 0.0000000000946401
08_BC 9.98861e-27
12_BF 0.000000262931
14_BG 5.81892e-16
15_01B 1.09532e-27
B 0.99955

Cross-Validation of Discriminant Models
Miss-Classification Rate: 10 / 300 at 10 Dimensional MDS
         Predicted
Objective 07_BC 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          1     1     0      0 283

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (major) Outlierness: 0.60537 (all), 0.375922 (group)
Subtype Posterior Probability
01_AE 2.01541e-30
A 1.60211e-21
B 1
C 1.49559e-29
D 0.000000000873594
F 6.38702e-22
G 1.65443e-23
H 8.36598e-31
J 3.82857e-18
K 6.58101e-22

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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for 5tat (nested) Outlierness: 0.367509 (all), 0.698489 (group)
Subtype Posterior Probability
03_AB 0.000993609
07_BC 2.00477e-17
08_BC 1.01091e-26
12_BF 0.000000889906
14_BG 3.07314e-20
15_01B 3.48225e-27
B 0.999005

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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for vpu (major) Outlierness: 0.538347 (all), 0.664569 (group)
Subtype Posterior Probability
01_AE 0.00000000000658929
A 0.00000000000485637
B 1
C 0.0000000000149351
D 0.000000354829
F 0.0000000396918
G 0.000000000000389067
H 0.00000000000350756
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

Download Multiple Alignment Distance Matrix GGobi XML

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 0.000000000000257778
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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (major) Outlierness: 0.8441 (all), 0.915409 (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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 0.883017 (all), 0.933507 (group)
Subtype Posterior Probability
03_AB 0.00062238
07_BC 0
08_BC 0
12_BF 1.41103e-39
14_BG 0.0000000000606797
15_01B 0.000000000000694235
B 0.999378

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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for nef (major) Outlierness: 0.743345 (all), 0.592351 (group)
Subtype Posterior Probability
01_AE 0
A 2.24885e-30
B 1
C 8.75189e-36
D 0.000000000000359931
F 5.07077e-24
G 0
H 1.20082e-31
J 2.24488e-42
K 1.87548e-27

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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for nef (nested) Outlierness: 0.625465 (all), 0.614104 (group)
Subtype Posterior Probability
03_AB 0
07_BC 1.09404e-31
08_BC 9.29061e-43
12_BF 6.15136e-17
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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for ltr (major) Outlierness: 0.871811 (all), 0.665682 (group)
Subtype Posterior Probability
01_AE 1.4013e-45
A 2.46499e-24
B 1
C 4.24201e-29
D 1.27904e-17
F 3.75732e-29
G 2.054e-38
H 3.71256e-21
J 6.36042e-40
K 2.74424e-28

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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for ltr (nested) Outlierness: 0.677014 (all), 0.641226 (group)
Subtype Posterior Probability
03_AB 0
07_BC 0
08_BC 0
12_BF 4.56823e-41
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

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Copyrighted by Bio-Data Mining Lab, Department of Bioinformatics and Life Sciences, Soongsil University, Seoul, Korea