TB-Profiler result

Run: SRR28351342
Summary

Run ID: SRR28351342

Sample name:

Date: 2024-05-22T10:11:07.394539

Number of reads: 1449846

Percentage reads mapped: 99.37

Median coverage: 36.0

Strain: lineage2.2.1;lineage4

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.88
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.89
lineage2.2 East-Asian (Beijing) RD105;RD207 0.86
lineage4 Euro-American None 0.1
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.71 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpsL 781687 p.Lys43Arg missense_variant 0.55 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
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 0.9 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.9 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.47 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.89 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575744 p.Ala133Thr missense_variant 0.78 ethionamide
isoniazid Uncertain significance
mshA 575749 c.402C>A synonymous_variant 0.81 ethionamide
isoniazid
mshA 575761 c.414C>G synonymous_variant 0.87 ethionamide
isoniazid
mshA 575764 c.417C>G synonymous_variant 0.87 ethionamide
isoniazid
mshA 575771 p.Val142Thr missense_variant 0.88 ethionamide
isoniazid
mshA 575776 c.429C>T synonymous_variant 0.85 ethionamide
isoniazid
mshA 575782 c.435G>C synonymous_variant 0.82 ethionamide
isoniazid
mshA 575785 c.438T>C synonymous_variant 0.82 ethionamide
isoniazid
mshA 575795 p.Ile150Val missense_variant 0.8 ethionamide
isoniazid
mshA 575800 c.453G>C synonymous_variant 0.8 ethionamide
isoniazid
mshA 575803 c.456C>T synonymous_variant 0.78 ethionamide
isoniazid Not assoc w R - Interim
mshA 575821 c.474G>T synonymous_variant 0.8 ethionamide
isoniazid
mshA 575837 c.490C>T synonymous_variant 0.8 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
mshA 575842 c.495G>C synonymous_variant 0.8 ethionamide
isoniazid
mshA 575864 c.517T>C synonymous_variant 0.75 ethionamide
isoniazid
mshA 575884 c.537G>C synonymous_variant 0.73 ethionamide
isoniazid
mshA 575893 c.546C>G synonymous_variant 0.67 ethionamide
isoniazid
ccsA 620625 p.Ile245Met missense_variant 0.86 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.88 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.89 ethionamide Uncertain significance
rpoB 760070 c.264T>C synonymous_variant 0.57 rifampicin
rpoB 760082 c.276C>T synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoB 760088 c.282C>G synonymous_variant 0.68 rifampicin
rpoB 760091 c.285G>C synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoB 760101 c.295T>C synonymous_variant 0.73 rifampicin Not assoc w R - Interim
rpoB 760104 c.298_300delTCGinsAGC synonymous_variant 0.73 rifampicin
rpoB 760112 c.306T>C synonymous_variant 0.77 rifampicin
rpoB 760118 c.312T>G synonymous_variant 0.79 rifampicin Not assoc w R - Interim
rpoB 760121 c.315T>C synonymous_variant 0.85 rifampicin Not assoc w R - Interim
rpoB 760130 p.Asp108Glu missense_variant 0.88 rifampicin Uncertain significance
rpoB 760136 c.330G>A synonymous_variant 0.88 rifampicin
rpoB 760139 c.333A>T synonymous_variant 0.89 rifampicin
rpoB 760142 c.336C>G synonymous_variant 0.91 rifampicin
rpoB 760178 c.372G>A synonymous_variant 0.93 rifampicin Not assoc w R - Interim
rpoB 760181 c.375T>C synonymous_variant 0.93 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.93 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.93 rifampicin Not assoc w R - Interim
rpoB 760235 c.429T>C synonymous_variant 0.94 rifampicin Not assoc w R - Interim
rpoB 760244 c.438G>C synonymous_variant 0.94 rifampicin Not assoc w R - Interim
rpoB 760283 c.477G>C synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rpoB 760298 c.492G>C synonymous_variant 0.88 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.91 rifampicin Not assoc w R
rpoC 765352 c.1983G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 765357 p.Met663Thr missense_variant 0.37 rifampicin
rpoC 765361 c.1992C>G synonymous_variant 0.41 rifampicin
rpoC 765383 c.2014_2016delATGinsCC frameshift_variant&missense_variant 0.63 rifampicin
rpoC 765403 c.2034G>C synonymous_variant 0.67 rifampicin
rpoC 765404 p.Leu679Lys missense_variant 0.67 rifampicin
rpoC 765409 c.2040T>C synonymous_variant 0.69 rifampicin
rpoC 765412 c.2043T>C synonymous_variant 0.69 rifampicin
rpoC 765425 p.Lys686Glu missense_variant 0.7 rifampicin
rpoC 765445 c.2076G>C synonymous_variant 0.81 rifampicin Not assoc w R - Interim
rpoC 765452 p.Ala695Arg missense_variant 0.78 rifampicin
rpoC 765466 c.2097C>T synonymous_variant 0.85 rifampicin
rpoC 765478 c.2109T>C synonymous_variant 0.82 rifampicin Not assoc w R - Interim
rpoC 765480 p.Tyr704Phe missense_variant 0.83 rifampicin Uncertain significance
rpoC 765496 c.2127C>G synonymous_variant 0.83 rifampicin
rpoC 765499 c.2130C>G synonymous_variant 0.83 rifampicin Not assoc w R - Interim
rpoC 765529 c.2160C>T synonymous_variant 0.72 rifampicin
rpoC 765533 p.Tyr722His missense_variant 0.71 rifampicin Uncertain significance
rpoC 765547 c.2178C>T synonymous_variant 0.66 rifampicin Not assoc w R - Interim
rpoC 765548 c.2179_2181delAGCinsTCG synonymous_variant 0.68 rifampicin
rpoC 765553 c.2184C>T synonymous_variant 0.67 rifampicin Not assoc w R - Interim
rpoC 765556 c.2187G>C synonymous_variant 0.67 rifampicin
rpoC 765562 c.2193G>T synonymous_variant 0.66 rifampicin Not assoc w R - Interim
rpoC 765577 c.2208G>T synonymous_variant 0.67 rifampicin
rpoC 765591 p.Arg741Gln missense_variant 0.5 rifampicin
rpoC 765596 p.Lys743Gln missense_variant 0.49 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.78 rifampicin Not assoc w R - Interim
rpoC 767104 c.3735C>G synonymous_variant 0.77 rifampicin Not assoc w R - Interim
rpoC 767105 c.3736_3738delAACinsCG frameshift_variant&missense_variant 0.77 rifampicin
rpoC 767119 c.3750A>G synonymous_variant 0.79 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>T synonymous_variant 0.76 rifampicin Not assoc w R - Interim
rpoC 767138 c.3769C>T synonymous_variant 0.76 rifampicin Not assoc w R - Interim
rpoC 767158 c.3789T>C synonymous_variant 0.79 rifampicin Not assoc w R - Interim
rpoC 767162 p.Asn1265Ala missense_variant 0.79 rifampicin
rpoC 767174 p.Asn1269Asp missense_variant 0.81 rifampicin
rpoC 767180 p.Ala1271Gln missense_variant 0.81 rifampicin
rpoC 767191 c.3822C>G synonymous_variant 0.84 rifampicin Not assoc w R - Interim
rpoC 767197 c.3828G>A synonymous_variant 0.82 rifampicin Not assoc w R - Interim
rpoC 767200 c.3831G>A synonymous_variant 0.8 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.95 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.92 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.88 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253930 p.Phe202Tyr missense_variant 0.24 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.95 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.75 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1673772 c.-430C>A upstream_gene_variant 0.51 ethionamide
isoniazid
inhA 1673778 c.-424C>G upstream_gene_variant 0.5 ethionamide
isoniazid
inhA 1673784 c.-418G>T upstream_gene_variant 0.51 ethionamide
isoniazid
inhA 1673787 c.-415G>C upstream_gene_variant 0.54 ethionamide
isoniazid
inhA 1673799 c.-403T>C upstream_gene_variant 0.53 ethionamide
isoniazid
inhA 1673802 c.-400A>G upstream_gene_variant 0.54 ethionamide
isoniazid
inhA 1673808 c.-394A>C upstream_gene_variant 0.55 ethionamide
isoniazid
fabG1 1673829 p.Asn130Lys missense_variant 0.61 ethionamide
isoniazid
fabG1 1673830 p.Lys131Arg missense_variant 0.61 ethionamide
isoniazid
inhA 1673838 c.-364T>C upstream_gene_variant 0.63 ethionamide
isoniazid
inhA 1673841 c.-361A>G upstream_gene_variant 0.63 ethionamide
isoniazid
fabG1 1673844 p.Met135Ile missense_variant 0.61 ethionamide
isoniazid
inhA 1673847 c.-355A>C upstream_gene_variant 0.61 ethionamide
isoniazid
inhA 1673853 c.-349A>C upstream_gene_variant 0.61 ethionamide
isoniazid
inhA 1673856 c.-346T>C upstream_gene_variant 0.61 ethionamide
isoniazid
inhA 1673859 c.-343G>C upstream_gene_variant 0.61 ethionamide
isoniazid
inhA 1673865 c.-337C>G upstream_gene_variant 0.66 ethionamide
isoniazid
fabG1 1673870 p.Ser144Met missense_variant 0.61 ethionamide
isoniazid
inhA 1673877 c.-325C>G upstream_gene_variant 0.59 ethionamide
isoniazid
fabG1 1673905 p.Ser156Ala missense_variant 0.58 ethionamide
isoniazid
inhA 1673916 c.-286A>C upstream_gene_variant 0.37 ethionamide
isoniazid
rpsA 1834177 c.636A>C synonymous_variant 0.87 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
katG 2154724 p.Arg463Leu missense_variant 0.86 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.89 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.21 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.87 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.81 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.92 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038551 c.2154C>G synonymous_variant 0.52 pyrazinamide
clpC1 4038563 c.2142C>T synonymous_variant 0.63 pyrazinamide
clpC1 4038584 c.2121G>A synonymous_variant 0.71 pyrazinamide
clpC1 4038587 c.2118C>G synonymous_variant 0.71 pyrazinamide
clpC1 4038596 c.2109A>G synonymous_variant 0.74 pyrazinamide
clpC1 4038602 c.2103G>C synonymous_variant 0.75 pyrazinamide
clpC1 4038623 c.2082A>G synonymous_variant 0.79 pyrazinamide
clpC1 4038640 p.Asp689Asn missense_variant 0.83 pyrazinamide
clpC1 4038647 c.2058T>G synonymous_variant 0.81 pyrazinamide
clpC1 4038658 p.Lys683Gln missense_variant 0.81 pyrazinamide
clpC1 4038660 c.2044_2045delTCinsAG synonymous_variant 0.81 pyrazinamide
clpC1 4038662 c.2043T>C synonymous_variant 0.79 pyrazinamide
clpC1 4038671 c.2034T>G synonymous_variant 0.78 pyrazinamide Not assoc w R - Interim
clpC1 4038679 p.Pro676Ala missense_variant 0.77 pyrazinamide
clpC1 4038683 c.2022T>C synonymous_variant 0.78 pyrazinamide Not assoc w R - Interim
clpC1 4038695 c.2010C>G synonymous_variant 0.75 pyrazinamide
clpC1 4038704 c.2001T>C synonymous_variant 0.69 pyrazinamide
clpC1 4038710 c.1995G>C synonymous_variant 0.66 pyrazinamide
clpC1 4038713 c.1992T>C synonymous_variant 0.63 pyrazinamide
clpC1 4038725 c.1980C>G synonymous_variant 0.66 pyrazinamide
clpC1 4038740 c.1965G>C synonymous_variant 0.58 pyrazinamide
clpC1 4039022 c.1683A>G synonymous_variant 0.58 pyrazinamide
clpC1 4039046 c.1659C>T synonymous_variant 0.74 pyrazinamide Not assoc w R - Interim
clpC1 4039064 c.1641C>T synonymous_variant 0.82 pyrazinamide
clpC1 4039067 c.1638G>C synonymous_variant 0.84 pyrazinamide
clpC1 4039079 c.1626C>G synonymous_variant 0.87 pyrazinamide Not assoc w R - Interim
clpC1 4039085 c.1620A>G synonymous_variant 0.88 pyrazinamide
clpC1 4039091 c.1614G>C synonymous_variant 0.89 pyrazinamide
clpC1 4039097 c.1608G>T synonymous_variant 0.9 pyrazinamide
clpC1 4039100 c.1605C>T synonymous_variant 0.9 pyrazinamide Not assoc w R - Interim
clpC1 4039103 c.1602T>C synonymous_variant 0.9 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.9 pyrazinamide
clpC1 4039118 c.1587C>A synonymous_variant 0.9 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.91 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.91 pyrazinamide
clpC1 4039169 c.1536A>G synonymous_variant 0.9 pyrazinamide
clpC1 4039178 c.1527G>C synonymous_variant 0.9 pyrazinamide
clpC1 4039183 c.1522T>C synonymous_variant 0.9 pyrazinamide
clpC1 4039187 c.1518G>T synonymous_variant 0.88 pyrazinamide
clpC1 4039190 c.1515C>G synonymous_variant 0.89 pyrazinamide
clpC1 4039220 c.1485G>C synonymous_variant 0.78 pyrazinamide
clpC1 4039729 p.Asp326Asn missense_variant 0.35 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249757 p.Thr1082Ala missense_variant 0.46 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.84 ethambutol Not assoc w R
ethA 4326906 p.Leu190Phe missense_variant 0.46 ethionamide Uncertain significance
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 0.81 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.86 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.79 streptomycin Not assoc w R