TB-Profiler result

Run: SRR1146278
Summary

Run ID: SRR1146278

Sample name:

Date: 2024-10-03T18:32:20.278370

Number of reads: 1064254

Percentage reads mapped: 99.33

Median coverage: 25.0

Strain: lineage2.2.1;lineage4

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.16
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.13
lineage2.2 East-Asian (Beijing) RD105;RD207 0.21
lineage4 Euro-American 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.Thr400Ala Uncertain significance Mutation from literature
p.Ser450Leu Assoc w R
isoniazid katG p.Ile335Val Uncertain significance Mutation from literature
p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Trp119Gly Assoc w R - Interim
streptomycin rpsL p.Lys43Arg 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
ethionamide ethA c.966_968dupGAC Mutation from literature
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 761004 p.Thr400Ala missense_variant 0.77 rifampicin Uncertain significance Mutation from literature
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.36 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.63 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155109 p.Ile335Val missense_variant 0.29 isoniazid Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288887 p.Trp119Gly missense_variant 0.67 pyrazinamide Assoc w R - Interim
embB 4247431 p.Met306Ile missense_variant 0.79 ethambutol Assoc w R
ethA 4326505 c.966_968dupGAC disruptive_inframe_insertion 0.47 ethionamide 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
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13656 c.-98C>A upstream_gene_variant 0.35 isoniazid Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.26 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.26 ethionamide Uncertain significance
rpoB 761889 p.Val695Leu missense_variant 0.72 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.38 rifampicin Not assoc w R
mmpL5 777875 c.605delG frameshift_variant 0.77 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801009 c.201A>G synonymous_variant 0.75 linezolid Not assoc w R - Interim
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.5 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 0.96 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.38 pyrazinamide Not assoc w R - Interim
ndh 2101831 c.1212G>A synonymous_variant 0.73 isoniazid Not assoc w R - Interim
delamanid Not assoc w R - Interim
ethionamide Not assoc w R - Interim
katG 2156173 c.-62C>A upstream_gene_variant 0.78 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.29 pyrazinamide Not assoc w R
Rv1979c 2223214 c.-50A>C upstream_gene_variant 0.77 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ahpC 2726141 c.-52C>A upstream_gene_variant 0.48 isoniazid Uncertain significance
Rv2752c 3065517 c.675C>T synonymous_variant 0.84 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 0.28 cycloserine
Rv3236c 3612219 p.Val300Ile missense_variant 0.83 pyrazinamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.32 pyrazinamide Not assoc w R - Interim
ethA 4326474 p.Pro334Ala missense_variant 0.29 ethionamide Uncertain significance
ethA 4328317 c.-844C>T upstream_gene_variant 0.78 ethionamide
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
gid 4407588 c.615A>G synonymous_variant 0.28 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.22 streptomycin Not assoc w R
gid 4407967 p.Leu79Trp missense_variant 0.81 streptomycin Uncertain significance