Table 3

T-RF diversity for single phylogenetic descriptions
Phylogenetic affiliation dTRF (bp) dTRF shifteda(bp) Countsb(−) Relative contribution to T-RFc(%) Reference OTUd Reference GenBank accession numbere SW mapping scoref(−) Normalized SW mapping scoreg(−)
Flocculent and aerobic granular sludge samples from wastewater treatment systems
Rhodocyclus tenuis 39 34 37 4.8 3160 AB200295 363 0.917
199 194 1 25.0 3160 AB200295 248 0.648
205 200 3 100.0 3160 AF204247 314 0.858
210 205 1 100.0 3160 AF204247 211 0.699
218 213 11 91.7 3160 AB200295 356 0.942
219 214 769 99.6 3160 AB200295 371 0.949
220 215 6 37.5 3160 AF502230 318 0.817
221 216 1 7.7 3160 AF502230 276 0.865
225 220 2 3.7 3160 AB200295 206 0.703
252 247 3 100.0 3160 AB200295 305 0.762
253 248 9 100.0 3160 AB200295 228 0.752
257 252 1 20.0 3160 AF502230 241 0.660
Groundwater samples from aquifers contaminated with chloroethenes
Dehalococcoides spp. 166 161 1 100.0 1368 EF059529 290 0.775
168 163 143 100.0 1368 EF059529 241 0.717
169 164 2 100.0 1368 EF059529 331 0.768
170 165 2 100.0 1368 EF059529 241 0.693
171 166 1 50.0 1368 EF059529 303 0.783
173 168 1 100.0 1368 EF059529 241 0.717
176 171 1 100.0 1369 DQ833317 211 0.687
179 174 1 100.0 1369 DQ833317 193 0.629
188 183 4 66.7 1369 DQ833340 464 0.947

a Digital T-RF obtained after having shifted the digital dataset with the most probable average cross-correlation lag.

b Number of reads of the target phylotype that contribute to the T-RF.

c Diverse bacterial affiliates can contribute to the same T-RF.

d Reference OTU from the Greengenes public database obtained after mapping.

e GenBank accession numbers provided by Greengenes for reference sequences.

f Best SW mapping score obtained.

g SW mapping score normalized by the read length.

Weissbrodt et al.

Weissbrodt et al. BMC Microbiology 2012 12:306   doi:10.1186/1471-2180-12-306

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