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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 0 227 169 A A A (Unambiguous Nested)


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
939876 CAA77499 gag 0 75 61 A A A (Major agrees Nested with high confidence)


Detailed result for gag (major) Outlierness: 0.74638 (all), 0.686273 (group)
Subtype Posterior Probability
01_AE 0.0000153083
A 0.999984
B 4.24684e-16
C 4.72935e-18
D 0.0000000000000576921
F 0.00000000000000594907
G 0.0000000000191326
H 0.000000000033003
J 0.000000000000511816
K 0.000000336602

Cross-Validation of Discriminant Models
Miss-Classification Rate: 28 / 1142 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    70   2   0   0   0   0   0   0   0
    A         3 127   0   0   2   0   1   0   0
    B         0   1 261   0   2   1   0   0   0
    C         0   0   0 553   0   0   0   0   0
    D         0   0   2   0  73   0   1   0   0
    F         0   0   0   0   0  10   0   3   2
    G         0   0   0   0   0   0  20   1   0
    H         0   0   0   0   1   2   0   0   0
    J         0   0   0   0   0   0   0   0   0
    K         0   2   0   0   0   0   0   1   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for gag (nested) Outlierness: 0.595832 (all), 0.581758 (group)
Subtype Posterior Probability
02_AG 0.000000000940939
03_AB 0.00104613
04_cpx 0.0000000636832
06_cpx 0.000000282778
09_cpx 0.000243498
11_cpx 0.00000191356
13_cpx 0.0000000362094
16_A2D 0.00000000196135
A 0.998708

Cross-Validation of Discriminant Models
Miss-Classification Rate: 29 / 225 at 10 Dimensional MDS
         Predicted
Objective 02_AG 03_AB 04_cpx 06_cpx 09_cpx 11_cpx 13_cpx 16_A2D   A
   02_AG     57     0      0      0      0      1      0      0   1
   03_AB      0     0      0      0      0      0      0      0   0
   04_cpx     0     0      1      2      0      0      0      0   0
   06_cpx     0     0      3      5      0      0      1      0   0
   09_cpx     0     0      0      0      0      0      0      0   5
   11_cpx     0     0      0      0      0      9      0      0   1
   13_cpx     0     0      0      2      0      0      1      0   0
   16_A2D     0     0      0      0      0      0      0      2   0
   A          1     2      1      0      3      2      1      2 121

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