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Locus HGDI All strains Beijing Non-Beijing Qubllb 0.830 0.731 0.714 Qub18 0.854 0.813 0.672 Qub26 0.800 0.632 0.907 MIRU26 0.799 0.655 0.832 Mtub21 0.790 0.705 0.469 Mtub04 0.647 0.397 0.604 ETR-F 0.633 0.451 0.507 MIRU31 0.630 0.277 0.334 MIRU10 0.570 0.162 0.274 Qub4156 0.533 0.625 0.228 MIRU40 0.476 0.243 0.639 Qub1895 0.363 0.368 0.356
In table 4, the allelic differences for MIRU loci had accounted based on HGDI statistic formula, that is loci 20, 24 and 27 had lower allele difference (HGDI [less than or equal to] 0.3), loci 31, 39 and 40 were in middle (0.3 [less than or equal to] HGDI [less than or equal to] 0.6) and loci 10, 16, 23 and 26 had the most allele difference among the locus MIRU (HGDI greater than or equal to] 0.6).
The mean 15 MIRU-ETR HGDI value for the Beijing family was low (0.163), which indicates that this family is relatively homogeneous, even within the diverse London population settings.
Thus, we performed spoligotyping in combination with MLVA and found a general HGDI score of 0.986 for this combined method.
Table 4: HGDI scores of the different MIRU-VNTR loci.
For all strains, genotyping with the 15-MIRU-ETR loci set was more informative and had a higher discriminatory power than with spoligotyping, as expected (HGDI 0.747 for MIRU vs 0.572 for spoligotyping, data not shown).
The 15-MIRU-ETR profiles 223325153533423 or 223325173533423 were shared by 106 (82.2%) of the total number of analyzed Beijing strains with an HGDI of 0.625 for all 15 loci.
The HGDI for 25 VNTR loci together was 0.870 (compared with 0.625 for the original set of MIRU-ETRs).
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