TB-Profiler result

Run: ERR11082694
Summary

Run ID: ERR11082694

Sample name:

Date: 11-04-2023 02:00:09

Number of reads: 830700

Percentage reads mapped: 99.68

Strain: lineage4.6.5

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (1.00)
Isoniazid R katG p.Ser315Thr (1.00), katG p.Gly307Glu (0.18)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.Trp68Cys (1.00)
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin R tlyA p.Asn236Lys (1.00)
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.5 Euro-American T;LAM None 1.0
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
tlyA 1918647 p.Asn236Lys missense_variant 1.0 capreomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155192 p.Gly307Glu missense_variant 0.18 isoniazid
pncA 2289038 p.Trp68Cys missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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
gyrB 5489 p.Ile84Val missense_variant 1.0
gyrB 5976 p.Val246Asp missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9036 p.Ala579Thr missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490756 c.-27T>G upstream_gene_variant 1.0
mshA 575772 p.Val142Ala missense_variant 0.18
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576114 p.Arg256Pro missense_variant 0.25
mshA 576751 c.1408delC frameshift_variant 0.12
rpoB 760685 p.Leu293Phe missense_variant 0.12
rpoB 761661 c.1855C>T synonymous_variant 0.14
rpoC 765966 p.Arg866His missense_variant 0.15
rpoC 766486 c.3117A>G synonymous_variant 0.13
rpoC 766619 p.Gln1084* stop_gained 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777119 p.His454Gln missense_variant 0.24
mmpL5 777122 c.1359C>T synonymous_variant 0.24
mmpL5 777128 c.1353A>G synonymous_variant 0.25
mmpL5 777974 c.507C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417274 p.Gly25Val missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673346 c.-94C>G upstream_gene_variant 0.23
fabG1 1673349 c.-91G>C upstream_gene_variant 0.26
fabG1 1673357 c.-83G>A upstream_gene_variant 0.26
fabG1 1673359 c.-81T>C upstream_gene_variant 0.26
fabG1 1673361 c.-79C>G upstream_gene_variant 0.26
fabG1 1673380 c.-60C>G upstream_gene_variant 0.26
rpsA 1834464 p.Gly308Asp missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102382 c.661C>T synonymous_variant 0.15
katG 2156400 c.-289G>A upstream_gene_variant 0.22
PPE35 2167814 c.2799C>T synonymous_variant 0.15
PPE35 2169902 p.Leu237Phe missense_variant 0.31
PPE35 2169910 p.Asn235Tyr missense_variant 0.33
Rv1979c 2222084 p.Leu361Phe missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746995 p.Val202Ile missense_variant 1.0
Rv3083 3449084 p.Pro194Leu missense_variant 0.25
Rv3083 3449240 p.Arg246His missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474226 p.Pro74Ser missense_variant 0.13
fbiA 3640346 c.-196delA upstream_gene_variant 1.0
rpoA 3878021 p.Pro163Ser missense_variant 0.12
rpoA 3878084 p.Arg142Cys missense_variant 0.15
clpC1 4038332 c.2373C>T synonymous_variant 1.0
clpC1 4039018 p.Ser563Ala missense_variant 0.15
clpC1 4039022 c.1683A>G synonymous_variant 0.16
clpC1 4039031 c.1674T>C synonymous_variant 0.21
clpC1 4040144 c.561G>C synonymous_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243550 c.318C>T synonymous_variant 0.12
aftB 4268012 c.825G>A synonymous_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407845 p.Glu120Lys missense_variant 0.18