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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
env 2 126 70 B B B (Major agrees Nested with high confidence)


Detailed result for env (major) Outlierness: 0.603985 (all), 0.645624 (group)
Subtype Posterior Probability
01_AE 0.00000825502
A 0.00000000010938
B 0.990907
C 0.00326602
D 0.0000000137784
F 0.00509586
G 0.000550264
H 0.000000085046
J 0.0000000000005177
K 0.000172799

Cross-Validation of Discriminant Models
Miss-Classification Rate: 156 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   G   J
    01_AE    68   0   2   0   0   0   0
    A         0  79   1   0   0   2   0
    B         1   0 446   6   1   0   0
    C         1   1  92 367   0   1   2
    D         0   0   7   1  52   0   0
    F         0   0  15   1   0   0   0
    G         0   1  13   2   0   7   0
    H         0   0   0   0   0   3   0
    J         0   0   0   0   0   0   0
    K         0   0   2   0   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 1.12907 (all), 1.14619 (group)
Subtype Posterior Probability
03_AB 0.0000241086
07_BC 0.000000107802
08_BC 0.0000000979708
12_BF 0.000599863
14_BG 0.0685392
15_01B 0.00199169
B 0.928845

Cross-Validation of Discriminant Models
Miss-Classification Rate: 31 / 484 at 10 Dimensional MDS
         Predicted
Objective 03_AB 07_BC 12_BF 15_01B   B
   03_AB      0     0     0      0   0
   07_BC      0     8     1      0   1
   08_BC      0     2     0      0   0
   12_BF      0     1     0      0   9
   14_BG      0     0     0      0   3
   15_01B     0     0     0      0   4
   B          1     5     1      2 445

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