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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 0 226 165 C C C (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
60100 CAA77491 gag 0 74 59 C C C (Major agrees Nested with high confidence)


Detailed result for gag (major) Outlierness: 0.848027 (all), 0.939975 (group)
Subtype Posterior Probability
01_AE 4.11637e-16
A 8.00752e-17
B 0.000000000000337811
C 1
D 6.34978e-20
F 1.26741e-19
G 5.53398e-20
H 1.98988e-18
J 8.83413e-16
K 1.52201e-18

Cross-Validation of Discriminant Models
Miss-Classification Rate: 20 / 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         1 129   0   0   2   0   1   0   0   0
    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: 1.06652 (all), 1.06522 (group)
Subtype Posterior Probability
07_BC 0.00000329082
08_BC 0.000436053
10_CD 2.09794e-21
C 0.999561

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