TB-Profiler result

Run: SRR10397238
Summary

Run ID: SRR10397238

Sample name:

Date: 2024-04-15T12:17:35.197715

Number of reads: 2527666

Percentage reads mapped: 99.58

Median coverage: 75.0

Strain: lineage4.2.1;lineage4.3.3

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.39
lineage4.2 Euro-American None 0.61
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) None 0.58
lineage4.3.3 Euro-American (LAM) RD115 0.4
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Leu27Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin eis c.-14C>T Assoc w R - Interim Can only confer resistance if genetically linked to a functional Eis
capreomycin
kanamycin eis c.-14C>T Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine ald c.436_437dupGC Mutation from literature
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
gyrA 7582 p.Asp94Ala missense_variant 0.31 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.49 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.39 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.37 isoniazid Assoc w R High-level resistance
pncA 2289162 p.Leu27Pro missense_variant 0.43 pyrazinamide Assoc w R
eis 2715346 c.-14C>T upstream_gene_variant 0.33 amikacin Assoc w R - Interim Can only confer resistance if genetically linked to a functional Eis
kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
ald 3087252 c.436_437dupGC frameshift_variant 0.36 cycloserine Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.41 ethambutol Assoc w R
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 8040 p.Gly247Ser missense_variant 0.31 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
fgd1 491247 c.465C>T synonymous_variant 0.64 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 656125 c.1345dupG frameshift_variant 0.37 ethionamide Uncertain significance
Rv0565c 656832 c.639G>A synonymous_variant 0.39 ethionamide Not assoc w R - Interim
rpoB 761032 p.Gln409Arg missense_variant 0.52 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.36 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.62 linezolid
fbiC 1302901 c.-30G>T upstream_gene_variant 0.63 clofazimine
pretomanid
delamanid
fbiC 1303095 c.165G>A synonymous_variant 0.43 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471892 n.47G>A non_coding_transcript_exon_variant 0.55 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1476222 n.2565A>C non_coding_transcript_exon_variant 0.61 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834836 p.Met432Thr missense_variant 0.43 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.78 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.58 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.39 isoniazid Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.56 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.36 isoniazid
ahpC 2726142 c.-51G>A upstream_gene_variant 0.42 isoniazid Uncertain significance
folC 2746340 p.Ala420Val missense_variant 0.37 para-aminosalicylic_acid
ribD 2987502 p.Gly222Ser missense_variant 0.43 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.39 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 0.62 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612696 p.Arg141Gly missense_variant 0.66 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.37 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.26 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.56 ethambutol Not assoc w R - Interim
ethA 4326593 p.Cys294Tyr missense_variant 0.46 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.61 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.48 streptomycin Not assoc w R