TB-Profiler result

Run: ERR108422
Summary

Run ID: ERR108422

Sample name:

Date: 19-10-2023 19:25:05

Number of reads: 5186088

Percentage reads mapped: 99.56

Strain: lineage4.3.3;lineage2.2.1

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.Asp435Tyr (0.86), rpoB p.Glu761Asp (0.18)
Isoniazid R fabG1 c.-8T>A (0.89), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (0.88)
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.-7T>C (0.14)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.13
lineage4 Euro-American LAM;T;S;X;H None 0.89
lineage4.3 Euro-American (LAM) mainly-LAM None 0.88
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.12
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.12
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.88
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 761109 p.Asp435Tyr missense_variant 0.86 rifampicin
rpoB 762089 p.Glu761Asp missense_variant 0.18 rifampicin
fabG1 1673432 c.-8T>A upstream_gene_variant 0.89 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.88 ethambutol
ethA 4327480 c.-7T>C upstream_gene_variant 0.14 ethionamide
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.83
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.15
rpoB 761172 p.Gly456Ser missense_variant 0.88
rpoC 763031 c.-339T>C upstream_gene_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 0.84
rpoC 766645 p.Glu1092Asp missense_variant 0.13
rpoC 766667 p.Ser1100Ala missense_variant 0.86
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.11
mmpL5 776182 p.Asp767Asn missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918681 p.Asp248Cys missense_variant 0.9
katG 2154724 p.Arg463Leu missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289226 p.Ile6Leu missense_variant 0.12
kasA 2518919 p.Gly269Ser missense_variant 0.9
pepQ 2860571 c.-153T>G upstream_gene_variant 0.9
thyA 3073868 p.Thr202Ala missense_variant 0.89
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339490 p.Leu125Ile missense_variant 0.86
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.16
clpC1 4038287 c.2418C>T synonymous_variant 0.85
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244823 p.Val531Leu missense_variant 0.86
embB 4248316 c.1803C>T synonymous_variant 0.91
aftB 4267647 p.Asp397Gly missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407877 p.Gly109Ala missense_variant 0.91
gid 4408156 p.Leu16Arg missense_variant 0.88