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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: 0.219922 (all), 0.243094 (group)
Subtype Posterior Probability
01_AE 0.00000183895
A 0.00000291626
B 0.605965
C 0.380846
D 0.0000000468871
F 0.010856
G 0.00204512
H 0.00000115833
J 0.00000000882151
K 0.000282446

Cross-Validation of Discriminant Models
Miss-Classification Rate: 215 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   G   H   J
    01_AE    65   1   3   0   0   0   0   1
    A         0  76   1   2   0   1   1   1
    B         1   0 412  39   1   1   0   0
    C         0   5 107 351   1   0   0   0
    D         0   0   6   3  51   0   0   0
    F         0   0   8   8   0   0   0   0
    G         0   2  10   6   0   5   0   0
    H         0   3   0   0   0   0   0   0
    J         0   0   0   0   0   0   0   0
    K         0   0   1   1   0   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 0.268204 (all), 0.239477 (group)
Subtype Posterior Probability
03_AB 0.00258319
05_DF 0.000248172
07_BC 0.00224362
08_BC 0.000514308
10_CD 0.0000000616457
12_BF 0.00501839
14_BG 0.000667621
15_01B 0.00320785
B 0.714748
C 0.261259
F 0.0095096

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