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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 0 227 166 C C C (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60102 CAA77493 gag 0 75 60 C C C (Unambiguous Nested)


Detailed result for gag (major) Outlierness: 0.616944 (all), 0.625672 (group)
Subtype Posterior Probability
01_AE 0.000000000000741426
A 0.0000000118906
B 0.000000000186787
C 1
D 0.00000000000000887107
F 0.0000000000332863
G 0.000000000000819294
H 0.000000000000842683
J 0.000000000339607
K 0.0000000000234286

Cross-Validation of Discriminant Models
Miss-Classification Rate: 21 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    70   2   0   0   0   0   0   0   0   0
    A         1 128   0   0   2   0   1   0   0   1
    B         0   1 262   0   1   1   0   0   0   0
    C         0   0   0 553   0   0   0   0   0   0
    D         0   2   1   0  72   0   1   0   0   0
    F         0   0   0   0   1  14   0   0   0   0
    G         0   0   0   0   0   0  21   0   0   0
    H         0   0   0   0   0   2   0   0   0   1
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   0   0   1   1   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 0.335766 (all), 0.343347 (group)
Subtype Posterior Probability
07_BC 0.000000980891
08_BC 0.0000174953
10_CD 3.98079e-20
C 0.999982

Cross-Validation of Discriminant Models
Miss-Classification Rate: 4 / 564 at 10 Dimensional MDS
         Predicted
Objective 07_BC 08_BC 10_CD   C
    07_BC     3     0     0   0
    08_BC     0     2     0   3
    10_CD     0     0     3   0
    C         1     0     0 552

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