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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 0 105 58 C C C (Major agrees Nested with high confidence)


Detailed result for env (major) Outlierness: 0.15482 (all), 0.290191 (group)
Subtype Posterior Probability
01_AE 0.0000002001
A 0.000000326872
B 0.472394
C 0.505783
D 0.00000000668861
F 0.0208311
G 0.000957921
H 0.000000176652
J 0.0000000145537
K 0.0000331131

Cross-Validation of Discriminant Models
Miss-Classification Rate: 212 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   G   J
    01_AE    66   1   2   0   0   0   1
    A         0  78   1   2   0   1   0
    B         1   0 412  39   1   1   0
    C         0   5 107 351   1   0   0
    D         0   0   6   3  51   0   0
    F         0   0   8   8   0   0   0
    G         0   2  10   6   0   5   0
    H         0   3   0   0   0   0   0
    J         0   0   0   0   0   0   0
    K         0   0   1   1   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 0.272151 (all), 0.299739 (group)
Subtype Posterior Probability
03_AB 0.0000393615
05_DF 0.0025823
07_BC 0.0217003
08_BC 0.00231816
10_CD 0.0000000509173
12_BF 0.0201271
14_BG 0.00424849
15_01B 0.00128198
B 0.362614
C 0.563949
F 0.0211389

Cross-Validation of Discriminant Models
Miss-Classification Rate: 202 / 970 at 10 Dimensional MDS
         Predicted
Objective 08_BC 10_CD 15_01B   B   C
   03_AB      0     0      0   0   0
   05_DF      0     0      0   0   3
   07_BC      0     0      0   1   9
   08_BC      0     0      0   0   2
   10_CD      0     1      0   2   0
   12_BF      0     0      0   2   8
   14_BG      0     0      0   2   1
   15_01B     0     0      0   4   0
   B          0     2      2 407  43
   C          1     3      1  99 360
   F          0     0      0   8   8

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