TB-Profiler result

Run: SRR18593214
Summary

Run ID: SRR18593214

Sample name:

Date: 2024-04-16T10:58:41.906316

Number of reads: 3821337

Percentage reads mapped: 98.98

Median coverage: 107.0

Strain: lineage2.2;lineage4.2.2.2

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 Euro-American (Ural) None 0.91
lineage2 East-Asian RD105 0.08
lineage4.2 Euro-American None 0.9
lineage2.2 East-Asian (Beijing) RD105;RD207 0.09
lineage4 Euro-American None 0.91
lineage4.2.2.2 Euro-American (Ural) None 0.89
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asp Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
p.Trp91Arg Uncertain significance Mutation from literature
ethambutol
pyrazinamide pncA p.Phe81Val Uncertain significance Mutation from literature
streptomycin rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine alr p.Leu113Arg Mutation from literature
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 761139 p.His445Asp missense_variant 0.93 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.89 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.14 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.16 isoniazid Assoc w R High-level resistance
katG 2155841 p.Trp91Arg missense_variant 0.94 isoniazid Uncertain significance Mutation from literature
pncA 2289001 p.Phe81Val missense_variant 0.94 pyrazinamide Uncertain significance Mutation from literature
alr 3841083 p.Leu113Arg missense_variant 0.83 cycloserine Mutation from literature
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 845 p.Ile282Thr missense_variant 0.95 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7581 p.Asp94Thr missense_variant 0.88 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8688 p.Ala463Ser missense_variant 0.91 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
mshA 576077 c.730C>T synonymous_variant 0.92 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.1 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.12 ethionamide Not assoc w R - Interim
Rv0565c 657425 p.Gly16Ser missense_variant 0.86 ethionamide Uncertain significance
rpoB 761489 c.1683G>A synonymous_variant 0.9 rifampicin Not assoc w R
rpoC 764585 p.Leu406Phe missense_variant 0.92 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.17 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.15 clofazimine Not assoc w R
bedaquiline 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 0.82 linezolid
Rv1129c 1254144 p.Thr131Pro missense_variant 0.84 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
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 2063685 c.1044G>A synonymous_variant 0.91 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.94 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2715400 c.-68C>T upstream_gene_variant 0.9 amikacin
kanamycin
ahpC 2726142 c.-51G>A upstream_gene_variant 0.95 isoniazid Uncertain significance
pepQ 2860556 c.-138C>T upstream_gene_variant 0.86 clofazimine
bedaquiline
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.95 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086742 c.-78A>C upstream_gene_variant 0.93 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448850 p.Trp116* stop_gained 0.88 ethionamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.12 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.11 ethambutol Not assoc w R
embB 4247429 c.916_918delATGinsGT frameshift_variant&missense_variant 0.1 ethambutol
ethA 4326773 p.Ala234Asp missense_variant 0.9 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.1 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.11 streptomycin Not assoc w R