TB-Profiler result

Run: SRR10380215
Summary

Run ID: SRR10380215

Sample name:

Date: 2024-10-05T11:35:12.763113

Number of reads: 3694368

Percentage reads mapped: 99.54

Median coverage: 118.0

Strain: lineage4.1.2.1;lineage4.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.35
lineage4.1.2 Euro-American None 0.33
lineage4.2 Euro-American None 0.66
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.38
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) None 0.64
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Ser297Ala Uncertain significance Mutation from literature
pyrazinamide
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 761155 p.Ser450Leu missense_variant 0.74 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.62 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.74 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.59 isoniazid Assoc w R High-level resistance
eis 2715344 c.-12C>T upstream_gene_variant 0.56 kanamycin Assoc w R
embB 4247402 p.Ser297Ala missense_variant 0.64 ethambutol Uncertain significance 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
fgd1 491247 c.465C>T synonymous_variant 0.6 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fgd1 491591 p.Lys270Met missense_variant 0.34 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.32 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 619969 p.Val27Ile missense_variant 0.61 kanamycin Uncertain significance
capreomycin Not assoc w R - Interim
amikacin Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.38 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.31 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.69 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.37 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 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 800204 c.-605T>C upstream_gene_variant 0.65 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834675 c.1134C>T synonymous_variant 0.31 pyrazinamide
tsnR 1854204 p.Arg200Gln missense_variant 0.3 linezolid
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 0.66 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.67 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2156219 c.-108A>T upstream_gene_variant 0.3 isoniazid Uncertain significance
PPE35 2169879 p.Phe245Cys missense_variant 0.64 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.34 isoniazid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.22 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.14 capreomycin
Rv2681 2997861 p.Pro375Ser missense_variant 0.33 capreomycin
ald 3086742 c.-78A>C upstream_gene_variant 0.6 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3623222 c.1689A>G synonymous_variant 0.65 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
lpqB 3624407 c.504C>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.36 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 0.34 ethambutol Not assoc w R
embA 4244849 c.1617C>T synonymous_variant 0.32 ethambutol Not assoc w R - Interim
embB 4249594 c.3081G>A synonymous_variant 0.59 ethambutol Not assoc w R - Interim
ethA 4326632 p.His281Pro missense_variant 0.65 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.62 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