TB-Profiler result

Run: SRR16915764
Summary

Run ID: SRR16915764

Sample name:

Date: 21-01-2024 12:01:02

Number of reads: 32298429

Percentage reads mapped: 99.62

Strain: lineage4.3.4.2;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.Ser450Leu (0.85)
Isoniazid R katG p.Ser315Thr (0.86)
Ethambutol R embB p.Met306Ile (0.83)
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.752dupG (0.83), ethA c.752dupG (0.83)
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 0.16
lineage4 Euro-American LAM;T;S;X;H None 0.84
lineage4.3 Euro-American (LAM) mainly-LAM None 0.84
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.16
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.16
lineage4.3.4 Euro-American (LAM) LAM RD174 0.84
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.83
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 0.85 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.86 isoniazid
embB 4247431 p.Met306Ile missense_variant 0.83 ethambutol
ethA 4326721 c.752dupG frameshift_variant 0.83 ethionamide, 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
gyrB 6140 p.Val301Leu missense_variant 0.82
gyrB 7087 p.Met616Ile missense_variant 0.83
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.16
ccsA 620625 p.Ile245Met missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 0.16
rpoC 764918 p.Val517Leu missense_variant 0.83
rpoC 764995 c.1626C>G synonymous_variant 0.82
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.14
Rv1258c 1406964 p.Ser126Trp missense_variant 0.16
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833469 c.-73G>T upstream_gene_variant 0.82
rpsA 1834177 c.636A>C synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 0.17
PPE35 2169750 p.Gly288Glu missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.82
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.82
Rv3236c 3612813 p.Thr102Ala missense_variant 0.13
alr 3840719 c.702A>G synonymous_variant 0.83
clpC1 4038287 c.2418C>T synonymous_variant 0.86
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.17
embB 4247028 p.Leu172Arg missense_variant 0.24
embB 4247033 p.Ser174Arg missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 0.16
ethA 4326676 p.Ser266Arg missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.17
gid 4407927 p.Glu92Asp missense_variant 0.16
gid 4407970 p.Pro78Leu missense_variant 0.83
gid 4408156 p.Leu16Arg missense_variant 0.81