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Volume 8, Number 11—November 2002

Dispatch

Genomewide Pattern of Synonymous Nucleotide Substitution in Two Complete Genomes of Mycobacterium tuberculosis

Austin L. Hughes*Comments to Author , Robert Friedman*, and Megan Murray†
Author affiliations: *University of South Carolina, Columbia, South Carolina, USA; †Harvard School of Public Health, Boston, Massachusetts, USA;

Main Article

Table 2

Proteins for which the nearest homologous comparison between the H37Rv and CDC1551 genotypes of Mycobacterium tuberculosis has a high pS value (Group B)

Accession nos. Protein function pS pN
Probable differential deletion
NP_216309, NP_335079 unknown 0.0470 0.0000
NP_215713, NP_335504 unknown 0.0628 0.0043
NP_216319, NP_336310 PE repeat family 0.0115 0.0094
NP_215965, NP_335949 PE repeat family 0.0448 0.0185
Possible horizontal gene transfer
NP_214910, NP_334815 unknown 0.0226 0.0105
NP_216104, NP_336077 unknown 0.0265 0.0084
NP_216281, NP_336535 unknown 0.0210 0.0161
NP_215835, NP_335809 adenylate cyclase 0.0229 0.0068
NP_216564, NP_336573 polyketide synthase 0.0093 0.0036
NP_217029, NP_337080 unknown 0.0148 0.0156
NP_216862, NP_335679 unknown 0.0313 0.0000
Mean ± S.E. 0.0286 ± 0.0050 0.0085 ±
0.0019a

aPaired sample t-test of the hypothesis that pS = pN , p<0.01. The quantities pS and pN are the proportion of nucleotide difference per synonymous site and per nonsynonymous site, respectively.

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