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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
pol 2 229 219 ? A A Undecided


Detailed result for pol (major) Outlierness: 4.85927 (all), 10.53 (group)
Subtype Posterior Probability
01_AE 0.0000000000023987
A 1
B 0
C 0
D 0
F 0
G 0
H 0
J 0
K 0

Cross-Validation of Discriminant Models
Miss-Classification Rate: 26 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    57   0   0   0   0   0   0   0   0   0
    A         7  51   0   0   0   0   1   0   0   0
    B         0   0 158   0   6   4   0   0   0   0
    C         0   0   0 370   0   0   0   0   0   1
    D         0   3   0   0  43   0   0   0   0   0
    F         0   0   0   0   1  11   0   0   0   0
    G         0   0   0   0   0   0  16   0   0   0
    H         0   0   0   0   0   0   0   1   2   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   0   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 7.43791 (all), 12.2316 (group)
Subtype Posterior Probability
02_AG 2.01787e-42
03_AB 0.00679907
04_cpx 5.17569e-17
06_cpx 0
09_cpx 0.0000000000280785
11_cpx 0
13_cpx 0
16_A2D 1.31089e-19
A 0.993201

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 130 at 10 Dimensional MDS
         Predicted
Objective 02_AG 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 16_A2D  A
   02_AG     40      0      3      0      0      0      0  0
   03_AB      0      0      0      0      0      0      0  0
   04_cpx     0      3      0      0      0      0      0  0
   06_cpx     0      0      5      0      0      0      0  0
   09_cpx     0      0      0      4      0      0      0  0
   11_cpx     0      0      0      0     10      0      0  0
   13_cpx     0      0      0      0      0      3      0  0
   16_A2D     0      0      0      0      0      0      2  0
   A          1      0      0      0      0      0      2 56

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