TB-Profiler result

Run: SRR11972358
Summary

Run ID: SRR11972358

Sample name:

Date: 2024-04-16T03:13:30.871432

Number of reads: 1690664

Percentage reads mapped: 81.16

Median coverage: 42.0

Strain: lineage1.2.2;lineage3.1.2

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.65
lineage1.2.2 Indo-Oceanic RD239 0.41
lineage3.1.2 East-African-Indian RD750 0.67
lineage1 Indo-Oceanic RD239 0.35
lineage3.1 East-African-Indian RD750 0.43
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 gyrB p.Glu501Asp Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Glu501Asp Assoc w R - Interim
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1054delG Assoc w R
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
gyrB 6742 p.Glu501Asp missense_variant 0.12 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethA 4326419 c.1054delG frameshift_variant 0.3 ethionamide 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
gyrB 5075 c.-165C>T upstream_gene_variant 0.39 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.56 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.27 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 7884 p.Arg195Cys missense_variant 0.42 levofloxacin
moxifloxacin
gyrA 8452 p.Ala384Val missense_variant 0.34 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.37 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
Rv0010c 13298 p.Ile87Met missense_variant 0.42 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.35 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.36 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.45 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.56 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.38 ethionamide
hadA 731724 c.-206A>G upstream_gene_variant 0.43 isoniazid
hadA 732367 c.438C>A synonymous_variant 0.41 isoniazid Not assoc w R - Interim
nusG 734116 c.-138T>C upstream_gene_variant 0.26 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.62 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.47 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.44 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.47 rifampicin Not assoc w R
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 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 800357 c.-452C>A upstream_gene_variant 0.31 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.41 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.57 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.22 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471820 n.-25delC upstream_gene_variant 0.6 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
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
tlyA 1918162 p.Glu75Lys missense_variant 0.34 capreomycin Uncertain significance
ndh 2103276 c.-234G>C upstream_gene_variant 0.47 ethionamide
delamanid
isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155269 c.843C>T synonymous_variant 0.37 isoniazid
PPE35 2167772 c.2841C>T synonymous_variant 0.62 pyrazinamide Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.64 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.47 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.44 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.47 clofazimine Not assoc w R
bedaquiline Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.69 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.77 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.46 isoniazid
ahpC 2725929 c.-264C>G upstream_gene_variant 0.62 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.34 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.57 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.65 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612984 p.Asn45His missense_variant 0.49 pyrazinamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.25 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.28 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.34 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.73 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.33 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4138622 c.1134C>T synonymous_variant 0.43 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.41 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.62 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245789 p.Thr853Ala missense_variant 0.63 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.56 ethambutol Not assoc w R
embB 4246979 p.Gly156Ser missense_variant 0.34 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.27 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.41 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.27 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.41 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.34 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.32 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
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 4338603 c.-82C>T upstream_gene_variant 0.35 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 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.53 streptomycin Not assoc w R