TB-Profiler result

Run: ERR11043505
Summary

Run ID: ERR11043505

Sample name:

Date: 2024-10-04T19:47:36.081874

Number of reads: 5316411

Percentage reads mapped: 99.47

Median coverage: 153.0

Strain: lineage4.2.2.1;lineage5

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2.1 Euro-American None 0.86
lineage4.2.2 Euro-American (Ural) None 0.85
lineage4.2 Euro-American None 0.85
lineage4 Euro-American None 0.86
lineage5 West-Africa 1 RD711 0.12
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Leu430Pro Assoc w R
p.Asp435Gly 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
ahpC c.-54C>T Uncertain significance Mutation from literature
ethambutol embB p.Gln497Lys Assoc w R
pyrazinamide pncA p.Cys72Arg Assoc w R
streptomycin gid c.258_259insG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1338A>C Mutation from literature
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
rpoB 761095 p.Leu430Pro missense_variant 0.11 rifampicin Assoc w R
rpoB 761110 p.Asp435Gly missense_variant 0.12 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761155 p.Ser450Leu missense_variant 0.81 rifampicin Assoc w R
rrs 1473183 n.1338A>C non_coding_transcript_exon_variant 0.11 amikacin Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.87 isoniazid Assoc w R High-level resistance
pncA 2289028 p.Cys72Arg missense_variant 0.2 pyrazinamide Assoc w R
ahpC 2726139 c.-54C>T upstream_gene_variant 0.15 isoniazid Uncertain significance Mutation from literature
embB 4248002 p.Gln497Lys missense_variant 0.86 ethambutol Assoc w R
gid 4407944 c.258_259insG frameshift_variant 0.82 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
dnaA 1131 c.1131C>A synonymous_variant 0.86 isoniazid Not assoc w R - Interim
gyrB 6446 p.Ala403Ser missense_variant 0.16 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
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 9143 c.1842T>C synonymous_variant 0.12 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
gyrA 9566 c.2265C>T synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.19 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 576077 c.730C>T synonymous_variant 0.88 isoniazid Not assoc w R
ethionamide Not assoc w R - Interim
mshA 576108 p.Ala254Gly missense_variant 0.24 isoniazid
ethionamide
Rv0565c 656421 c.1050G>A synonymous_variant 0.15 ethionamide
hadA 732110 p.Cys61Gly missense_variant 0.9 isoniazid Uncertain significance
rpoB 760677 p.Glu291Lys missense_variant 0.17 rifampicin Uncertain significance
rpoB 760994 c.1188G>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.11 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.16 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.88 linezolid
Rv1129c 1254056 p.Asp160Ala missense_variant 0.15 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.11 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.11 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.12 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1853565 c.-41G>A upstream_gene_variant 0.16 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 2062922 p.Ile603Val missense_variant 0.16 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063685 c.1044G>A synonymous_variant 0.89 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.84 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
ndh 2101921 c.1122G>A synonymous_variant 0.15 isoniazid Not assoc w R - Interim
delamanid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.15 isoniazid
eis 2714510 c.823T>C synonymous_variant 0.15 kanamycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2681 2996491 c.-248G>A upstream_gene_variant 0.18 capreomycin
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.84 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
ald 3086742 c.-78A>C upstream_gene_variant 0.87 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3624486 p.Asp142Gly missense_variant 0.16 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840932 c.489C>T synonymous_variant 0.13 cycloserine
ddn 3986987 c.144G>T synonymous_variant 0.12 pretomanid
delamanid Not assoc w R - Interim
ddn 3987180 p.Asp113Asn missense_variant 0.12 pretomanid
delamanid Uncertain significance
clpC1 4040824 c.-120C>T upstream_gene_variant 0.15 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.13 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4239334 c.-529T>C upstream_gene_variant 0.89 ethambutol Not assoc w R
embC 4239843 c.-20A>C upstream_gene_variant 0.11 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.13 ethambutol Not assoc w R
embA 4245147 p.Pro639Ser missense_variant 0.16 ethambutol Not assoc w R - Interim
embB 4247465 p.Asn318Asp missense_variant 0.18 ethambutol Uncertain significance
embB 4247646 p.Glu378Ala missense_variant 0.17 ethambutol Not assoc w R
embB 4248616 c.2103G>T synonymous_variant 0.15 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 0.18 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.16 ethambutol Not assoc w R
ethA 4326533 p.Thr314Ile missense_variant 0.88 ethionamide Uncertain significance
ethA 4326977 p.His166Pro missense_variant 0.11 ethionamide Uncertain significance
ethA 4327103 p.Gly124Asp missense_variant 0.18 ethionamide Uncertain significance
ethA 4328322 c.-849G>T upstream_gene_variant 0.16 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.11 streptomycin Not assoc w R
gid 4407947 p.Leu86Phe missense_variant 0.19 streptomycin Uncertain significance