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Table 1 Genes Involved in strain-specific deletions.

From: Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments

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 PPE37metH (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)
  1. 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.