TB-Profiler result

Run: SRR28393663
Summary

Run ID: SRR28393663

Sample name:

Date: 2024-10-04T18:39:18.835997

Number of reads: 3064652

Percentage reads mapped: 99.63

Median coverage: 88.0

Strain: lineage4.1.1;lineage4.1.2.1;lineage4.3.4.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.37
lineage4.1 Euro-American None 0.64
lineage4.1.2 Euro-American None 0.16
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.18
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 0.44
lineage4.3.4 Euro-American (LAM) RD174 0.37
lineage4.3.4.2 Euro-American (LAM) RD174 0.35
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
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.Met306Val Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide pncA p.Val130Met Assoc w R - Interim
p.Val21Gly Assoc w R - Interim
p.Gln10Pro Assoc w R
streptomycin rrs n.513C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA p.Arg292* Assoc w R
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 761110 p.Asp435Val missense_variant 0.38 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.63 rifampicin Assoc w R
rrs 1472358 n.513C>T non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance Mutation from literature
inhA 1673425 c.-777C>T upstream_gene_variant 0.21 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 0.85 isoniazid Assoc w R High-level resistance
pncA 2288854 p.Val130Met missense_variant 0.4 pyrazinamide Assoc w R - Interim
pncA 2289180 p.Val21Gly missense_variant 0.4 pyrazinamide Assoc w R - Interim
pncA 2289213 p.Gln10Pro missense_variant 0.2 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.14 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.47 ethambutol Assoc w R
ethA 4326600 p.Arg292* stop_gained 0.54 ethionamide 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 0.53 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 7221 p.Ser661Thr missense_variant 0.45 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 491591 p.Lys270Met missense_variant 0.22 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.17 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.64 ethionamide Uncertain significance
rpoB 759939 p.Pro45Ser missense_variant 0.25 rifampicin Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.17 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.37 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.59 rifampicin Not assoc w R
rpoC 766487 p.Pro1040Ser missense_variant 0.51 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781276 c.-284A>C upstream_gene_variant 0.14 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.44 linezolid
Rv1129c 1254588 c.-54T>G upstream_gene_variant 0.33 levofloxacin
moxifloxacin
isoniazid
rifampicin
embR 1416699 p.Leu217Val missense_variant 0.4 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833674 p.Lys45Glu missense_variant 0.24 pyrazinamide Uncertain significance
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 2155612 p.Phe167Cys missense_variant 0.26 isoniazid 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 0.19 isoniazid
folC 2747453 p.Arg49Gln missense_variant 0.33 para-aminosalicylic_acid
Rv2752c 3065615 p.Asp193Asn missense_variant 0.45 levofloxacin
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3066898 c.-707C>T upstream_gene_variant 0.42 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyA 3073868 p.Thr202Ala missense_variant 0.35 para-aminosalicylic_acid
thyA 3074588 c.-117A>G upstream_gene_variant 0.54 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.41 pyrazinamide Not assoc w R
Rv3236c 3612846 p.Pro91Ser missense_variant 0.2 pyrazinamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrA 3627511 c.-162C>G upstream_gene_variant 0.43 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.39 pyrazinamide Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.13 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 0.68 ethambutol Not assoc w R
embA 4244741 c.1509C>T synonymous_variant 0.23 ethambutol Not assoc w R - Interim
embB 4249408 c.2895G>A synonymous_variant 0.47 ethambutol Not assoc w R
ethA 4326116 p.Thr453Ile missense_variant 0.5 ethionamide 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 4338600 c.-79T>C upstream_gene_variant 0.36 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407809 p.Asp132Tyr missense_variant 0.31 streptomycin Uncertain significance
gid 4408054 p.Leu50Arg missense_variant 0.38 streptomycin Uncertain significance
gid 4408125 p.Leu26Phe missense_variant 0.17 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.39 streptomycin Not assoc w R