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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: 0.669736 (all), 0.7188 (group)
Subtype Posterior Probability
01_AE 0.00000114431
A 0.00000108898
B 0.519604
C 0.450493
D 0.0000000000816709
F 0.0252998
G 0.00458832
H 0.000000436706
J 0.0000000032675
K 0.0000128186

Cross-Validation of Discriminant Models
Miss-Classification Rate: 214 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   G   H   J
    01_AE    66   0   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: 0.759802 (all), 0.991436 (group)
Subtype Posterior Probability
03_AB 0.0000825475
05_DF 0.00128202
07_BC 0.00530536
08_BC 0.00143659
10_CD 0.00000907311
12_BF 0.0192337
14_BG 0.0115432
15_01B 0.000509293
B 0.528482
C 0.412331
F 0.0197846

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