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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 0 111 58 B B B (Major agrees Nested with high confidence)


Detailed result for env (major) Outlierness: 0.542011 (all), 0.735917 (group)
Subtype Posterior Probability
01_AE 0.000728804
A 0.000579746
B 0.946226
C 0.0196659
D 0.0000000000405408
F 0.00930301
G 0.0232971
H 0.000050828
J 0.0000530624
K 0.0000959592

Cross-Validation of Discriminant Models
Miss-Classification Rate: 214 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   G   J
    01_AE    66   1   2   0   0   0   1
    A         0  78   1   2   0   1   0
    B         2   0 411  39   1   1   0
    C         0   5 106 351   1   1   0
    D         0   0   7   3  50   0   0
    F         0   0   8   8   0   0   0
    G         0   2  10   6   0   5   0
    H         0   3   0   0   0   0   0
    J         0   0   0   0   0   0   0
    K         0   0   1   1   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 0.604219 (all), 0.736011 (group)
Subtype Posterior Probability
02_AG 0.0000983848
03_AB 0.0000344934
04_cpx 0.00000532755
06_cpx 0.00153532
07_BC 0.00153333
08_BC 0.0000639569
09_cpx 0.0000193709
10_CD 0.0000000092066
11_cpx 0.00108059
12_BF 0.00377249
13_cpx 0.000571987
14_BG 0.0029952
15_01B 0.00100702
B 0.94895
C 0.0222337
G 0.0160991

Cross-Validation of Discriminant Models
Miss-Classification Rate: 241 / 1056 at 10 Dimensional MDS
         Predicted
Objective 02_AG 03_AB 04_cpx 07_BC 08_BC 09_cpx 10_CD 11_cpx 13_cpx   B   C   G
   02_AG     45     0      1     0     0      0     0      7      0   0   0   2
   03_AB      0     0      0     0     0      0     0      0      0   0   0   0
   04_cpx     3     0      0     0     0      0     0      0      0   0   0   0
   06_cpx     0     0      0     0     0      0     0      0      0   0   0   6
   07_BC      0     0      0     0     0      0     0      0      0   1   9   0
   08_BC      0     0      0     0     0      0     0      0      0   0   2   0
   09_cpx     3     0      0     0     0      0     1      0      0   0   0   0
   10_CD      0     0      0     0     0      0     0      0      0   2   1   0
   11_cpx     3     0      0     0     0      0     0      7      1   0   0   0
   12_BF      0     0      0     0     0      0     0      0      0   2   8   0
   13_cpx     1     0      0     0     0      0     0      1      0   0   0   1
   14_BG      0     0      0     0     0      0     0      0      0   2   1   0
   15_01B     0     0      0     0     0      0     0      0      0   4   0   0
   B          0     1      0     1     0      0     3      1      0 406  42   0
   C          1     0      0     0     1      2     3      1      0 104 351   1
   G          2     0      0     0     0      0     0      0      0   6   9   6

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