Table 1.
Genes Involved in strain-specific deletions.
| Position | Size | Genes Involved |
| H37Rv | ||
| 1987985 | 6830 | MT1800 (Glycosyl transferase) – MT1801 (Molybdopterin oxidoredutase) – mmpL14 (Transmembrane transport protein) |
| CDC1551 | ||
| 206981 | 58 | Rv0175 (Probable conserved MCE Associated membrane protein) |
| 888687 | 875 | Rv0792c (GNTR-Family transcriptional regulatory protein) – Rv0793 (Hypothetical protein) – Rv0794c (Putative oxidoreductase) |
| 2161299 | 139 | PPE34 |
| 2349725 | 58 | Intergenic Region between pepE (Xaa-Pro Dipeptidase) and Rv2090 (5'-3' Exonuclease) |
| 2373345 | 58 | C-terminal end of the Rv2112c (Hypothetical protein) |
| 2382265 | 2275 | PPE37 – metH (Methionine synthase) |
| 2701639 | 501 | Rv2406c (Conserved hypothetical protein) – Intergenic region – Rv2407 (Ribonuclease Z) |
| 3727960 | 5284 | PPE54 (Possible recombination event with PE-PGRS49-50 and PPE55) |
| 3732032 | 192 | PPE54 |
| 3948252 | 640 | Rv3519 (Conserved hypothetical protein) |
| F11 | ||
| 374076 | 61 | PPE5 |
| 1509585 | 1101 | Rv1334 (Conserved Hypothetical protein – Rv1335 (CFP10A) – cysM (cysteine synthetase) |
| 1890753 | 172 | Possible Promoter region of Rv1668c (Probable Macrolide ABC transport. ATP binding protein) |
| 2381228 | 2645 | PE22 and Intergenic region |
| 3183106 | 109 | Rv2859c (Hypothetical amidotransferase) |
| 3702663 | 104 | Intergenic region between lpdA (dihydrolipoamide dehydrogenase) and Rv3304 (Conserved hypothetical protein) |
| Haarlem | ||
| 912152 | 92 | Rv0823c (Possible transcriptional regulatory Protein) |
| 965426 | 481 | PE-PGRS15 |
| 1451173 | 115 | Intergenic region betwwen thrB (Homoserine kinase) and thrC (Threonine synthase) |
| 1521604 | 4753 | Rv1353c (Probable transcriptional regulatory protein) – Rv1354c (Possible diguanylate cyclase protein) – moeY (Molibdopterin biosynthesis protein) – Rv1356c (Hypothetical protein) |
| 2060412 | 643 | PE-PGRS33 |
| 2365930 | 1774 | helZ (Helicase) – Rv2102 (Conserved hypothetical protein) |
| 2546849 | 6480 | Rv2271 (Hypothetical protein) – Rv2272 (Probable conserved transmembrane protein) – Rv2273 (Probable conserved transmembrane protein) – Rv2274c (Hypothetical protein) – Rv2275 (Hypothetical protein) – cyp121 (Cytochrome P450) – Rv2277c (Probable glycerolphosphodiesterase) |
| 2792261 | 170 | PE-PGRS42 |
| 3117314 | 439 | Repeat region (DR) Intergenic between Rv2813 and Rv2814 |
| 3192481 | 87 | IS1539 Transposase contained in repeat region |
| 4033587 | 616 | Rv3600c (Conserved hypothetical protein) – panD (Aspartate decarboxylase precursor) |
| 4365135 | 84 | PPE69 and Intergenic region with PE36 |
| C | ||
| 334840 | 6611 | PE-PGRS3-PE-PGRS4-PPE3 (partially absent in Haarlem Strain) |
| 474110 | 125 | Rv0401 (Probable conserved transmembrane protein) |
| 565404 | 113 | Intergenic region between Rv0480c (Probable amidohydrolase) and Rv0481c (Hypothetical protein) |
| 956083 | 54 | Intergenic region between ercc3 (Probable DNA helicase) and Rv0862c (Hypothetical protein) |
| 1984522 | 109 | C-terminal end wag22 (PE-PGRS) |
| 2354142 | 214 | PE-PGRS36 |
| 2456125 | 115 | Intergenic region between qcrB (Ubiquinol cytochrome C reductase) and Rv2197c (Probable conserved transmembrane protein) |
| 2825166 | 53 | Rv2517c (Hypothetical protein) |
| 2914707 | 115 | PE-PGRS44 |
| 3113322 | 736 | Repeat region DR Intergenic between Rv2816c and Rv2817c |
| 3182209 | 54 | Intergenic region between frr (ribosome releasing factor) and pyrH (Uridylate kinase) |
| 3369008 | 113 | PPE47 |
| 3369190 | 81 | PPE48 |
| 3369344 | 62 | PE29 |
| 3369422 | 171 | PE29 |
| 3426378 | 83 | Rv3074 (Hypothetical protein) |
| 3911404 | 11522 | fadD17 (Fatty-acid-CoA Synthase)-PE-PGRS53-PE-PGRS54 |
| 4009833 | 3486 | clpC1 (Probable ATP-dependent protease) – lsr2 (Probable Iron-regulated protein) – lysS (lysyl t-RNA synthetase) |
| 4143780 | 560 | Rv3728 (Probable conserved two domain membrane protein – drug transporter) |
Gene names are according to Tuberculist http://genolist.pasteur.fr/TubercuList/ and for genes absent in the MTB H37Rv genome the names are according to the MTB CDC1551 genome annotation [12]. Position indicated correspond to the site where the deletion has occurred.