TB-Profiler result

Run: SRR1048996
Summary

Run ID: SRR1048996

Sample name:

Date: 2024-04-14T00:35:30.555716

Number of reads: 493561

Percentage reads mapped: 13.39

Median coverage: 11.0

Strain: lineage4.5

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.98
lineage4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 762917 c.3111C>G synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.38 rifampicin
rpoB 762929 c.3123G>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 762939 c.3133_3135delATGinsCC frameshift_variant&missense_variant 0.38 rifampicin
rpoB 762942 p.Ile1046Val missense_variant 0.38 rifampicin Uncertain significance
rpoC 762965 c.-405T>C upstream_gene_variant 0.43 rifampicin
rpoC 762980 c.-390T>C upstream_gene_variant 0.32 rifampicin
rpoC 764348 p.Met327Leu missense_variant 0.35 rifampicin
rpoC 764355 p.Gln329Pro missense_variant 0.38 rifampicin
rpoC 764377 c.1008C>G synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764383 c.1014C>G synonymous_variant 0.4 rifampicin
rpoC 764387 c.1018_1020delTTGinsCC frameshift_variant&missense_variant 0.35 rifampicin
rpoC 764398 c.1029G>C synonymous_variant 0.33 rifampicin
rpoC 764405 c.1036_1038delAGGinsCC frameshift_variant&missense_variant 0.33 rifampicin
rpoC 764410 c.1041G>T synonymous_variant 0.35 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
fbiC 1305446 p.Gly839Ala missense_variant 0.89 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472181 n.336G>A non_coding_transcript_exon_variant 0.62 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.61 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.67 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.67 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.67 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.57 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.57 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472690 n.845C>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin
rrs 1472861 n.1016G>C non_coding_transcript_exon_variant 0.93 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.43 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473149 n.1304G>C non_coding_transcript_exon_variant 0.5 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473162 n.1317C>G non_coding_transcript_exon_variant 0.5 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.5 streptomycin Not assoc w R
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.46 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.5 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.5 capreomycin
linezolid
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.45 capreomycin
linezolid
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.52 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.67 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.7 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.76 capreomycin
linezolid
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.72 capreomycin
linezolid
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.68 capreomycin
linezolid
rrl 1476455 n.2798C>G non_coding_transcript_exon_variant 0.63 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.55 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.57 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.59 capreomycin Not assoc w R
linezolid Uncertain significance
katG 2155626 c.486G>C synonymous_variant 0.3 isoniazid
katG 2155637 p.Leu159Ile missense_variant 0.35 isoniazid
katG 2155641 p.Lys157Arg missense_variant 0.36 isoniazid
katG 2155650 c.462G>A synonymous_variant 0.43 isoniazid Not assoc w R - Interim
katG 2155655 p.Lys153Gln missense_variant 0.43 isoniazid Uncertain significance
katG 2155661 p.Val151Ile missense_variant 0.52 isoniazid
katG 2155668 c.444G>C synonymous_variant 0.52 isoniazid
PPE35 2167892 c.2721G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
ahpC 2726744 c.552G>A synonymous_variant 1.0 isoniazid Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 1.0 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245567 p.Glu779Gln missense_variant 1.0 ethambutol Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin