TB-Profiler result

Run: SRR28394226
Summary

Run ID: SRR28394226

Sample name:

Date: 2024-10-04T12:22:17.301680

Number of reads: 4002444

Percentage reads mapped: 99.56

Median coverage: 110.0

Strain: lineage2.2.1;lineage4.1.1

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.82
lineage4.1 Euro-American None 0.16
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.8
lineage2.2 East-Asian (Beijing) RD105;RD207 0.81
lineage4 Euro-American None 0.18
lineage4.1.1 Euro-American (X-type) None 0.17
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 embB p.Met306Val Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
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
gyrA 7570 p.Ala90Val missense_variant 0.19 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Gly missense_variant 0.8 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.84 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.82 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Val missense_variant 0.73 ethambutol 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
gyrB 6052 p.Ile271Met missense_variant 0.19 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 7221 p.Ser661Thr missense_variant 0.12 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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 0.91 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.79 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.82 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.8 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.81 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.22 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.77 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.15 rifampicin Not assoc w R
rpoC 766467 p.Glu1033Ala missense_variant 0.2 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.82 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.8 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.78 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.19 linezolid
Rv1129c 1254131 p.Glu135Gly missense_variant 0.83 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.78 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.87 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1416699 p.Leu217Val missense_variant 0.29 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833594 p.Ser18Tyr missense_variant 0.21 pyrazinamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.83 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
katG 2154724 p.Arg463Leu missense_variant 0.75 isoniazid Not assoc w R
katG 2154832 p.Leu427Pro missense_variant 0.14 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.82 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
Rv2752c 3065683 p.Asp170Gly missense_variant 0.21 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3065756 c.435delC frameshift_variant 0.82 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
thyA 3074588 c.-117A>G upstream_gene_variant 0.17 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449381 p.Trp293* stop_gained 0.17 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.83 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.8 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627511 c.-162C>G upstream_gene_variant 0.21 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3877949 p.Thr187Ala missense_variant 0.87 rifampicin Uncertain significance
glpK 4138614 p.Ile381Thr missense_variant 0.29 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4139183 c.572dupG frameshift_variant 0.68 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.16 ethambutol Not assoc w R
embA 4243217 c.-16C>A upstream_gene_variant 0.17 ethambutol Uncertain significance
embA 4243460 c.228C>T synonymous_variant 0.8 ethambutol Not assoc w R
embA 4245621 p.Ala797Pro missense_variant 0.15 ethambutol Uncertain significance
embB 4249408 c.2895G>A synonymous_variant 0.21 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.81 ethambutol Not assoc w R
ethA 4326116 p.Thr453Ile missense_variant 0.14 ethionamide Uncertain significance
ethA 4326273 p.Phe401Val missense_variant 0.15 ethionamide Uncertain significance
ethA 4327416 p.Ala20Ser missense_variant 0.78 ethionamide Uncertain significance
ethA 4327445 p.Val10Gly missense_variant 0.77 ethionamide Uncertain significance
whiB6 4338409 p.Pro38Leu missense_variant 0.85 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin 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
gid 4407588 c.615A>G synonymous_variant 0.82 streptomycin Not assoc w R
gid 4407797 p.Ser136Pro missense_variant 0.13 streptomycin Uncertain significance
gid 4407927 p.Glu92Asp missense_variant 0.8 streptomycin Not assoc w R