TB-Profiler result

Run: SRR21576614
Summary

Run ID: SRR21576614

Sample name:

Date: 2024-10-04T22:18:37.294478

Number of reads: 1294101

Percentage reads mapped: 98.51

Median coverage: 70.0

Strain: lineage4.5

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 1.0
lineage4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG c.-10A>C Uncertain significance Mutation from literature
ahpC c.-54C>T Uncertain significance Mutation from literature
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Asp12Asn Assoc w R - Interim
streptomycin gid c.-284_51del Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Glu427* 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2156121 c.-10A>C upstream_gene_variant 0.98 isoniazid Uncertain significance Mutation from literature
pncA 2289208 p.Asp12Asn missense_variant 1.0 pyrazinamide Assoc w R - Interim
ahpC 2726139 c.-54C>T upstream_gene_variant 1.0 isoniazid Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol Assoc w R
ethA 4326195 p.Glu427* stop_gained 1.0 ethionamide Assoc w R
gid 4408151 c.-284_51del start_lost&conservative_inframe_deletion 0.98 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 7892 c.591G>A synonymous_variant 0.98 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 1.0 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv0565c 656127 p.Tyr448* stop_gained 1.0 ethionamide Uncertain significance
rpoC 764817 p.Val483Gly missense_variant 1.0 rifampicin Uncertain significance
rpoC 766789 c.3420G>A synonymous_variant 1.0 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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
PPE35 2170568 p.Ile15Met missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640372 c.-171A>G upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoA 3879070 c.-563G>A upstream_gene_variant 1.0 rifampicin
clpC1 4038318 p.Pro796Leu missense_variant 1.0 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269296 p.Met180Val missense_variant 1.0 ethambutol Uncertain significance
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