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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 J F Undecided


Detailed result for env (major) Outlierness: 3.8119 (all), 3.4e38 (group)
Subtype Posterior Probability
01_AE 0.000000000019783
A 2.79836e-16
B 0.00423665
C 0.0000119165
D 8.22984e-21
F 0.273739
G 0.000040222
H 0.000000080945
J 0.721972
K 0.0000000000298245

Cross-Validation of Discriminant Models
Miss-Classification Rate: 218 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   G   H   J
    01_AE    69   0   1   0   0   0   0   0
    A         0  76   0   3   0   1   1   1
    B         0   0 409  42   3   0   0   0
    C         0   4 107 351   1   1   0   0
    D         0   0   9   4  47   0   0   0
    F         0   0   8   8   0   0   0   0
    G         0   2  10   6   0   5   0   0
    H         0   2   0   0   0   1   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: 5.16173 (all), 6.94216 (group)
Subtype Posterior Probability
05_DF 0.00000000000603794
06_cpx 0
11_cpx 1.23643e-39
12_BF 0.0000196309
13_cpx 4.83679e-38
F 0.99998
J 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 21 / 50 at 10 Dimensional MDS
         Predicted
Objective 05_DF 06_cpx 11_cpx 12_BF 13_cpx F
   05_DF      3      0      0     0      0 0
   06_cpx     0      6      0     0      0 0
   11_cpx     0      0      9     0      2 0
   12_BF      2      0      0     2      0 6
   13_cpx     0      0      3     0      0 0
   F          1      0      0     6      0 9
   J          0      0      0     0      0 0

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