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Table 1 List of CNVs identified via WGS and Sanger resequencing

From: The mutation rate of mycobacterial repetitive unit loci in strains of M. tuberculosisfrom cynomolgus macaque infection

MIRU locus Read depth candidate strains Mate pair candidate strains Copy numbers
154-A None None 1
154-B None None 2
424 None None 2
577 None None 2
580 A-3 None 3
802 H-3 H-3 3; (H-3 = 4)
960-A I-2 None 3
960-B None None 1
1644 None None 3
1955-A None None 1
1955-B None None 1
2059 None None 1
2163b None None 3
2165* None None 3
2347 None None 1
2401-A None None 3
2401-B None None 1
2461 None None 2
2531-A None None 1
2531-B None None 1
2687-A None None 1
2687-B None None 1
2996 None C-1 5
3007 None None 3
3171* None None 2
3192 G-3 C-1 2; (G-3 = 1)
3690 None C-1 5
4052 None None 3
4156 None None 3
4348 None None 2
  1. Loci containing asterisks (2165 and 3171) were only analyzed using Sanger sequencing. Bolded strains (H-3 at locus 802 and G-3 at locus 3192) were confirmed insertion and deletion events, respectively, via Sanger resequencing. Discrete copy numbers for each strain were determined by Sanger sequencing. Previous strain notation is used [17].