TB-Profiler result

Run: SRR25827331
Summary

Run ID: SRR25827331

Sample name:

Date: 2024-10-04T06:16:54.609285

Number of reads: 40879322

Percentage reads mapped: 99.18

Median coverage: 1148.5

Strain: lineage3.1.2;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
lineage3 East-African-Indian RD750 0.8
lineage3.1.2 East-African-Indian RD750 0.79
lineage4.1 Euro-American None 0.19
lineage4 Euro-American None 0.19
lineage4.1.1 Euro-American (X-type) None 0.21
lineage3.1 East-African-Indian RD750 0.82
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.Met306Ile Assoc w R
pyrazinamide
streptomycin gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ser91Pro Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ser91Pro 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 7572 p.Ser91Pro missense_variant 0.78 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)
rpoB 761155 p.Ser450Leu missense_variant 0.8 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.74 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.81 ethambutol Assoc w R
gid 4408100 c.102delG frameshift_variant 0.79 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
dnaA 429 c.429C>T synonymous_variant 0.2 isoniazid Not assoc w R - Interim
gyrB 5560 c.321C>A synonymous_variant 0.83 levofloxacin
moxifloxacin
gyrB 7221 p.Ser661Thr missense_variant 0.19 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 9212 c.1911G>A synonymous_variant 0.19 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13436 c.123A>G synonymous_variant 0.21 isoniazid Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.82 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.78 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.19 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.78 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.76 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.83 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.76 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.21 rifampicin Not assoc w R
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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.23 linezolid
rplC 800492 c.-317G>A upstream_gene_variant 0.8 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.8 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1407150 p.Thr64Ser missense_variant 0.21 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
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
katG 2154724 p.Arg463Leu missense_variant 0.84 isoniazid Not assoc w R
PPE35 2168453 c.2160C>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
PPE35 2168742 p.Gly624Asp missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.79 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.77 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.78 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.81 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2477c 2784426 c.-384G>A upstream_gene_variant 0.76 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878641 c.-135delG upstream_gene_variant 0.21 rifampicin Uncertain significance
rpoA 3878897 c.-390T>C upstream_gene_variant 0.23 rifampicin Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.8 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.8 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.81 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.19 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.19 ethambutol
embB 4247039 p.Phe176Val missense_variant 0.16 ethambutol
embB 4249408 c.2895G>A synonymous_variant 0.24 ethambutol Not assoc w R
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 0.75 streptomycin Not assoc w R