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Table 1 Polymorphic minisatellite markers for the M. tuberculosis complex

From: High resolution, on-line identification of strains from the Mycobacterium tuberculosis complex based on tandem repeat typing

Locus name "MIRU" alias [8] "ETR" alias [7] "QUB" alias [9, 11] Other alias Reference TR location on H37Rv genome Expected length in H37Rv (copy number) Expected length in CDC1551 (copy number) Expected length in M bovis AF2122 (copy number) N° of strains Size range observed (copy number) N° of alleles observed Polymorphism index
H37Rv_0024_18 bp     Mtub01 This report 24648 328 (10) 310 (9) 310 (9) 92 274–328 bp (7–10) 4 0.48
H37Rv_0079_9 bp     Mtub02 This report 79503 230 (6) 239 (7) 239 (7) 92 221–275 bp (5–11) 7 0.76
H37Rv_0154_53 bp MIRU2     [8] 154111 508 (2) 508 (2) 508 (2) 92 455–561 bp (1–3) 3 0.09
H37Rv_0424_51 bp     Mtub04 This report 424010 269 (2.6) 371 (4.6) 269 (2.6) 28 218 – 320 (1.6–3.6) 3 0.52
H37Rv_0531_15 bp     MPTR-A [7] 531430 328 (16) 328 (16) 328 (16) 48 (15–17) 3 0.23
H37Rv_0577_58 bp   ETR-C    [8] 577172 346 (4) 288 (3) 404 (5) 92 230–404 bp (2–5) 4 0.63
H37Rv_0580_77 bp MIRU4 ETR-D    [7] 580546 353 (3.3) 330 (3) 483 (5) 92 253–715 bp (2–8) 7 0.35
H37Rv_0802_54 bp MIRU40     [8] 802194 199 (1) 415 (5) 253 (2) 92 199–469 bp (1–6) 5 0.71
H37Rv_0959_53 bp MIRU10     [8] 959868 643 (3) 750 (5) 590 (2) 92 537–1014 bp (1–10) 9 0.76
H37Rv_1121_15 bp     Mtub12 This report 1121658 215 (4) 230 (5) 215 (4) 92 200–230 bp (3–5) 3 0.19
H37Rv_1443_56 bp     Mtub16 This report 1443417 291 (1) 347 (2) 347 (2) 11 291–515 (1–5) 3 0.56
H37Rv_1451_57 bp    QUB-1451c   [9] 1451778 305 (3.8) 305 (3.8) 305 (3.8) 56 (2–4) (bovis) 2 0.12
H37Rv_1612_21 bp    QUB-23   [11] 1612529 141 (5) 162 (6) 162 (6) 20 141–203 (5–8) 3 0.18
H37Rv_1644_53 bp MIRU16     [8] 1644026 671 (2) 724 (3) 671 (2) 92 618–777 bp (1–4) 4 0.59
H37Rv_1895_57 bp    QUB-1895   [9] 1895344 319 (4) 205 (2) 319 (4) 56 (2–4) (bovis) 3 0.35
H37Rv_1955_57 bp     Mtub21 This report 1955580 206 (2) 263 (3) 263 (3) 92 149–491 bp (1–7) 7 0.76
H37Rv_1982_78 bp    QUB-18   [11] 1982873 621 (5) 777 (7) 465 (3) 24 387–1167 (2–12) 9 0.74
H37Rv_2059_77 bp MIRU20     [8] 2059429 591 (2) 591 (2) 591 (2) 53 (1–2) 2 0.29
H37Rv_2074_56 bp*     Mtub24 This report 2074431 805 (3.6) 693 (1.6) 693 (1.6) 44 637–749 (0.6–2.6) 3 0.52
H37Rv_2163_a_69 bp    QUB-11a pUCD1 [11] 2163607 305 (3) 581 (7) 788 (10) 92 305–1832 bp (3–26) 15 0.88
H37Rv_2163_b_69 bp    QUB-11b pUCD1 [11] 2163729 412 (5) 274 (3) 343 (4) 52 136–826 (1–11) 8 0.82
H37Rv_2165_75 pb   ETR-A    [7] 2165223 397 (3) 322 (2) 847 (9) 92 322–847 bp (2–9) 8 0.73
H37Rv_2347_57 bp     Mtub29 This report 2347393 350 (4) 292 (3) 293 (3) 92 236–350 bp (2–4) 3 0.55
H37Rv_2401_58 bp     Mtub30 This report 2401815 319 (2) 435 (4) 435 (4) 92 261–435 bp (1–4) 3 0.55
H37Rv_2461_57 bp   ETR-B    [7] 2461279 292 (3) 235 (2) 406 (5) 92 178–406 bp (1–5) 6 0.51
H37Rv_2531_53 bp MIRU23     [8] 2531560 873 (6) 820 (5) 767 (4) 92 608–979 bp (1–8) 7 0.60
H37RV_2387_54 bp MIRU24     [8] 2684427 447 (1) 447 (1) 447 (1) 53 (1–2) 2 0.24
H37Rv_2990_55 bp     Mtub31 This report 2990582 257 (2) 312 (3) 312 (3) 49 202–312 bp (1–3) 3 0.15
H37Rv_2996_51 bp MIRU26     [8] 2996002 614 (3) 716 (5) 716 (5) 57 563–818 (2–7) 5 0.61
H37Rv_3006_53 bp MIRU27   QUB-5   [8] 3006875 657 (3) 657 (3) 657 (3) 92 551–710 bp (1–4) 4 0.25
H37Rv_3171_54 bp     Mtub34 This report 3171465 279 (3) 225 (2) 279 (3) 11 171–225 (1–2) 2 0.3
H37Rv_3192_53 bp MIRU31 ETR-E    [7] 3192168 651 (3) 651 (3) 651 (3) 92 545–810 bp (1–6) 6 0.67
H37Rv_3232_56 bp    QUB-3232   [9] 3232649 591 (3) 760 (6) 703 (5) 56 (4–22) (bovis) 10 0.65
H37Rv_3239_79 bp   ETR-F    [7] 3239469 476 (2.8) 476 (2.8) 421 (2.1) 48 (1–3) 3 0.49
H37Rv_3336_59 bp    QUB-3336   [9] 3336499 407 (5) 466 (6) 289 (3) 56 (3–21) (bovis) 8 0.55
H37Rv_3663_63 bp**     Mtub38 This report 3663751 373 (2.7) 310 (1.7) 310 (1.7) 92 247–400 bp (0.7–3.1) 5 0.35
H37Rv_3690_58 bp*     Mtub39 This report 3690947 341 (2.6)* 397 (3.6) 341 (2.6) 92 247–1349 bp (1–20)* 11 0.64
H37Rv_4052_111 bp    QUB-26   [11] 4052969 708 (5) 819 (6) 597 (4) 100 (4–14) (bovis) 5 0.41
H37Rv_4156_59 bp    QUB-4156c   [9] 4156797 224 (2) 283 (3) 165 (1) 52 106–283 (0–3) 4 0.69
H37Rv_4348_53 bp MIRU39     [8] 4348401 646 (2) 646 (2) 646 (2) 92 593–699 bp (1–3) 3 0.31
  1. The markers are listed according to their position in the H37Rv genome. The proposed reference name includes the size of the repeat unit. The twenty-one markers used in the present report are italicised and underlined. Alias names identified in the literature are indicated. QUB11a, QUB11b, and ETR-A (position 2163–2165) are located within the gene PPE34 [19]. The expected length assumes that the primers listed in Table 2 were used. * : the observed size (Table 3) is not the expected size. ** : the repeat unit is not easily defined, size variations do not correspond to a multiple of 63 base-pairs. Polymorphism index is calculated as 1 - ∑ (allele frequency)2 among the 86 distinct genotypes. The values are deduced from the original report in nine cases (indicated by the absence of size range in the "size range" column). In some instances [9, 11], the population of strains used is biased (M. bovis strains).