TB-Profiler result

Run: ERR3077998
Summary

Run ID: ERR3077998

Sample name:

Date: 2024-03-25T20:35:20.990100

Number of reads: 7304480

Percentage reads mapped: 99.46

Median coverage: 209.0

Strain: lineage3.1.1;lineage4.2.2.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.14
lineage3 East-African-Indian RD750 0.83
lineage3.1.1 East-African-Indian RD750 0.84
lineage4.2 Euro-American None 0.16
lineage4 Euro-American None 0.15
lineage4.2.2.2 Euro-American (Ural) None 0.14
lineage3.1 East-African-Indian RD750 0.82
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Gln432Glu Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Leu Assoc w R
p.Gln497Arg Assoc w R
p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA p.Val128Gly Assoc w R
p.Glu111* Assoc w R
streptomycin rpsL p.Lys88Met Assoc w R
gid c.471delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1265_1266insT 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
rpoB 761100 p.Gln432Glu missense_variant 0.13 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761155 p.Ser450Leu missense_variant 0.86 rifampicin Assoc w R
rpsL 781822 p.Lys88Met missense_variant 0.18 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288859 p.Val128Gly missense_variant 0.82 pyrazinamide Assoc w R
pncA 2288911 p.Glu111* stop_gained 0.15 pyrazinamide Assoc w R
embB 4247429 p.Met306Leu missense_variant 0.14 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.84 ethambutol Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 0.87 ethambutol Uncertain significance Mutation from literature
ethA 4326208 c.1265_1266insT frameshift_variant 0.85 ethionamide Assoc w R
gid 4407731 c.471delG frameshift_variant 0.83 streptomycin 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 8688 p.Ala463Ser missense_variant 0.23 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 491742 c.960T>C synonymous_variant 0.88 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576077 c.730C>T synonymous_variant 0.11 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.84 ethionamide Not assoc w R - Interim
Rv0565c 657425 p.Gly16Ser missense_variant 0.2 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.84 rifampicin Not assoc w R
rpoB 761248 p.Glu481Ala missense_variant 0.13 rifampicin Uncertain significance
rpoB 761407 p.Val534Ala missense_variant 0.89 rifampicin Uncertain significance
rpoB 762434 c.2628T>G synonymous_variant 0.84 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.82 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 0.86 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 0.16 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.81 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475259 n.1602T>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
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 0.18 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 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.88 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.87 pyrazinamide Not assoc w R
PPE35 2170461 p.Gly51Glu missense_variant 0.88 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
pncA 2289047 c.195C>T synonymous_variant 0.84 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.84 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.86 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.83 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
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.16 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086742 c.-78A>C upstream_gene_variant 0.19 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.84 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.85 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 4240172 p.Val104Met missense_variant 0.88 ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.84 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.86 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243323 p.Val31Ile missense_variant 0.84 ethambutol Uncertain significance
ethR 4328051 p.Ala168Val missense_variant 0.8 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
whiB6 4338846 c.-325T>G upstream_gene_variant 0.84 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.86 streptomycin Not assoc w R