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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 B B B (Major agrees Nested with high confidence)


Detailed result for env (major) Outlierness: 0.126481 (all), 0.428454 (group)
Subtype Posterior Probability
01_AE 0.00000404735
A 0.000000374047
B 0.906935
C 0.0844077
D 0.000000609035
F 0.00776845
G 0.000644672
H 0.000000231776
J 0.0000000905666
K 0.000239129

Cross-Validation of Discriminant Models
Miss-Classification Rate: 214 / 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         2   0 411  39   1   1   0
    C         0   5 106 351   1   1   0
    D         0   0   7   3  50   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: 0.31296 (all), 0.272163 (group)
Subtype Posterior Probability
03_AB 0.000191327
07_BC 0.00111741
08_BC 0.000104421
10_CD 0.00000000376756
12_BF 0.00200276
14_BG 0.00278079
15_01B 0.0125709
B 0.932533
C 0.0486996

Cross-Validation of Discriminant Models
Miss-Classification Rate: 184 / 951 at 10 Dimensional MDS
         Predicted
Objective 03_AB 08_BC 10_CD 15_01B   B   C
   03_AB      0     0     0      0   0   0
   07_BC      0     0     0      0   1   9
   08_BC      0     0     0      0   0   2
   10_CD      0     0     1      0   2   0
   12_BF      0     0     0      0   2   8
   14_BG      0     0     0      0   2   1
   15_01B     0     0     0      0   4   0
   B          1     0     2      2 407  42
   C          0     1     3      1 100 359

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