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

Virus: HIV-1 / Sequence Type: Protein

Sequence Description: (Link to NCBI GenPept)

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
pol 0 99 79 ? B B B (Unambiguous Nested)


Detailed result for pol (major) Outlierness: 0.579163 (all), 0.557385 (group)
Subtype Posterior Probability
01_AE 0.00000100679
A 0.00000000731713
B 0.999055
C 0.00000143032
D 0.000942048
F 0.00000092915
G 0.0000000000191176
H 0.0000000000000369049
J 6.84158e-25
K 0.0000000000281534

Cross-Validation of Discriminant Models
Miss-Classification Rate: 82 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    50   5   0   1   0   0   0   1   0
    A        14  39   0   1   0   0   4   1   0
    B         0   0 149   1  13   3   0   0   2
    C         1   0   4 363   0   0   0   3   0
    D         4   0   7   0  33   2   0   0   0
    F         1   0   1   1   0   7   0   0   2
    G         3   4   0   0   0   0   8   1   0
    H         1   0   0   0   0   0   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 pol (nested) Outlierness: 0.360798 (all), 0.344122 (group)
Subtype Posterior Probability
03_AB 0.000000000000226351
07_BC 0.000020235
08_BC 0.000000000249765
12_BF 0.000000529794
14_BG 0.00000000000000125759
15_01B 0.000000000327783
B 0.999979

Cross-Validation of Discriminant Models
Miss-Classification Rate: 12 / 184 at 10 Dimensional MDS
         Predicted
Objective 03_AB 07_BC 08_BC 12_BF 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     0     8      1   0
   14_BG      0     0     0     0      0   0
   15_01B     1     1     0     1      0   0
   B          0     0     1     3      0 164

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