TB-Profiler result

Run: SRR7755696
Summary

Run ID: SRR7755696

Sample name:

Date: 2024-04-16T04:00:03.605269

Number of reads: 2291524

Percentage reads mapped: 99.41

Median coverage: 45.0

Strain: lineage2.2.1;lineage4.2.1.1

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 0.26
lineage4.2 Euro-American None 0.75
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.23
lineage2.2 East-Asian (Beijing) RD105;RD207 0.27
lineage4 Euro-American None 0.81
lineage4.2.1.1 Euro-American (TUR) None 0.7
lineage4.2.1 Euro-American (TUR) None 0.62
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 p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.Cys14Arg Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Asn379Asp Assoc w R - Interim
clofazimine
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
thyA p.Arg222Gly Mutation from literature
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 0.32 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.45 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.38 isoniazid Assoc w R High-level resistance
pncA 2289202 p.Cys14Arg missense_variant 0.24 pyrazinamide Assoc w R
thyX 3067961 c.-16C>T upstream_gene_variant 0.44 para-aminosalicylic_acid Mutation from literature
thyA 3073808 p.Arg222Gly missense_variant 0.47 para-aminosalicylic_acid Mutation from literature
ethA 4326339 p.Asn379Asp missense_variant 0.26 ethionamide Assoc w R - Interim
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
gyrB 6768 p.Gly510Asp missense_variant 0.24 levofloxacin Uncertain significance
moxifloxacin
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
fgd1 491742 c.960T>C synonymous_variant 0.32 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.2 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.3 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.24 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.19 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.24 rifampicin Not assoc w R
rpoC 766779 p.Glu1137Gly missense_variant 0.35 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 0.35 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.33 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpL5 777451 p.Val344Leu missense_variant 0.71 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpR5 779100 c.111T>C synonymous_variant 0.84 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.28 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.65 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.34 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254582 c.-48A>C upstream_gene_variant 0.63 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
atpE 1460876 c.-169G>A upstream_gene_variant 0.75 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476091 n.2434T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673401 c.-801G>A upstream_gene_variant 0.85 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.24 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 0.7 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 0.71 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.31 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.36 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.62 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2752c 3067157 c.-966G>T upstream_gene_variant 0.76 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3086742 c.-78A>C upstream_gene_variant 0.73 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3623652 p.Pro420Leu missense_variant 0.72 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3641810 c.276G>C synonymous_variant 0.17 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.22 ethambutol Not assoc w R
whiB6 4338594 c.-73T>G upstream_gene_variant 0.43 capreomycin
amikacin
kanamycin
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 0.33 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.29 streptomycin Not assoc w R
gid 4408213 c.-11C>T upstream_gene_variant 0.47 streptomycin Uncertain significance