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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
gag 0 343 238 B B B (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.421841 (all), 0.663431 (group)
Subtype Posterior Probability
01_AE 5.92138e-29
A 8.23383e-26
B 1
C 3.42856e-20
D 0.00000000727781
F 1.51045e-17
G 5.07907e-37
H 2.75476e-31
J 2.43157e-19
K 1.14389e-17

Cross-Validation of Discriminant Models
Miss-Classification Rate: 11 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    72   0   0   0   0   0   0   0   0   0
    A         0 131   0   0   0   0   1   1   0   0
    B         0   0 263   0   1   1   0   0   0   0
    C         0   0   0 551   0   0   0   0   2   0
    D         0   1   1   0  74   0   0   0   0   0
    F         0   0   0   0   0  15   0   0   0   0
    G         0   0   0   0   0   0  21   0   0   0
    H         0   0   0   0   0   0   0   3   0   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   2   0   0   0   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 1.05819 (all), 1.34521 (group)
Subtype Posterior Probability
03_AB 3.75987e-28
07_BC 2.77552e-22
08_BC 3.20037e-26
12_BF 0.00000000130028
14_BG 7.59846e-26
15_01B 1.81258e-41
B 1

Cross-Validation of Discriminant Models
Miss-Classification Rate: 8 / 290 at 10 Dimensional MDS
         Predicted
Objective 07_BC 08_BC 12_BF 15_01B   B
   03_AB      0     0     0      0   0
   07_BC      1     2     0      0   0
   08_BC      1     4     0      0   0
   12_BF      0     0     8      0   2
   14_BG      0     0     0      0   0
   15_01B     0     0     0      5   0
   B          0     0     1      0 264

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