Skip to main content

Table 5 Statistical analysis of phenotypic and genotypic variability within each cluster containing 6 or more members.

From: A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes

NUM Phenotype #Seqs Intra_Pheno P_Pheno Intra_Geno P_Geno Avg_Muts Shared_Muts Shan._Ent.
1 444444444 15 0.69 0 6.15 0.47 9.1 4.95 14.52
2 444444442 28 0.56 0 7.31 0.02 8.3 3.4 18.78
4 444433433 10 0.64 0 7.83 0.05 8.7 3.84 18.33
5 444444413 6 0.63 2E-04 9.63 0.001 9.8 3.9 18.33
6 444433342 6 0.81 7E-04 7.07 0.27 7.7 3.33 13.74
7 444443422 31 0.8 0 7.5 0.008 7 2.43 19
9 444433422 7 0.63 0 8.31 0.04 8.6 3.79 16.91
12 444423402 6 0.65 2E-04 7.82 0.12 7.8 3.04 15.73
14 444232421 10 0.91 1E-04 6.61 0.34 5.9 2.19 14.14
16 444233401 8 0.82 1E-04 6.54 0.38 6.4 2.36 13.84
20 444222221 8 1.01 2E-04 6.18 0.49 5.2 1.41 13.84
26 442121211 13 0.85 0 4.11 0.05 3 0.71 9.88
29 321111111 9 0.8 0 2.38 7E-03 1.3 0.07 5.64
34 111010110 71 0.65 0 0.94 0 0.5 0.03 2.95
35 301000011 6 0.64 2E-04 0.67 3E-03 1 0.67 1.48
36 000000000 77 0.6 0 0.24 0 0.1 0 0.89
  1. "Phenotype" is the nine-digit shorthand describing the binned level of resistance of the cluster centroid toward each of the nine drugs (see Fig. 1 for drug order). "Intra Pheno" is the average intra-cluster phenotypic distance (in scaled resistance unites). "P pheno" are p-values for intra-cluster phenotypic distance. A p-value of 0 indicates that a more extreme distance was not sampled in 10,000 trials. Analogous headings are shown for genotypic distance as well; genotypic distance was defined using the list of non-polymorphic positions in the Methods. "Avg Muts" is the average number of mutations at non-polymorphic positions for sequences within the cluster. "Shared Muts" is the average number of shared mutations between all pairs within a cluster. Shan. Ent. is the computed Shannon Entopy (in bits) for the cluster, adding up the entropies at each non-polymorphic position.