Table 2 Comparisons of Indels calls by UVP and validated variants previously shown to be present in given isolates.

From: Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase

Sample IDPubMed IDAffected geneH37Rv reference genomic positionIndelUVP inferred IndelLineage informationtap gene(Rv1258c) frameshift mutation
ERR50292927021327dfrA, thyA3073130–3074471complete deletioncomplete deletion2.2.1present
ERR75136127021327Wt3073130–3074471no deletionno deletion2.2.1present
ERR75145327021327dfrA, thyA3073130–3074471complete deletioncomplete deletion2.2.1present
ERR75148327021327Wt3073130–3074471no deletionno deletion2.2.1present
ERR77537327021327dfrA, thyA3073130–3074471complete deletioncomplete deletion2.2.1present
ERR77991027021327dfrA, thyA3073130–3074471complete deletioncomplete deletion2.2.1present
SRR233321527021327dfrA, thyA3073130–3074471complete deletioncomplete deletion2.2.2absent
SRR195272125977398pncA2288681–2289241complete deletioncomplete deletion2.2.1present
SRR194817725977398pncA2288681–2289241complete deletioncomplete deletion2.2.1present
R721_C1326496891atsD756970C > CGC > CG2.2.1.1present
R721_C1326496891regX3581317G > GCGG > GCG2.2.1.1present
R966_C526496891Rv38614338065AC > AAC > A2.2.1present
R160_C1326496891adhD3452173CG > CGCCATCG > CGCCATG4.1.1.3absent
R376_C1126496891Rv3256c3636924ACC > ACACC > AC4.1.2.1absent
R912_C1126496891yrbE4A3920814GA > GGAA > GA1.2.2absent
R965_C126496891adhA2110232A > AGAG > AGG2.2.1present
R458_C326496891espR4323810GC > GGC > G4.1.2absent
R641_C126496891Rv23752655550A > ATAT > ATT2.2.1.1present