TB-Profiler result

Run: ERR10877882
Summary

Run ID: ERR10877882

Sample name:

Date: 2024-10-05T14:39:42.086693

Number of reads: 3346755

Percentage reads mapped: 99.64

Median coverage: 157.0

Strain: lineage4.2.1;lineage4.3.3

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 0.76
lineage4.2 Euro-American None 0.21
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) None 0.2
lineage4.3.3 Euro-American (LAM) RD115 0.78
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.Gln497Arg Assoc w R
pyrazinamide pncA p.Asp63Gly Assoc w R - Interim
streptomycin rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin tlyA p.Leu74Pro Uncertain significance Mutation from literature
kanamycin
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 0.73 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.83 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.82 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)
tlyA 1918160 p.Leu74Pro missense_variant 0.73 capreomycin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.86 isoniazid Assoc w R High-level resistance
pncA 2289054 p.Asp63Gly missense_variant 0.78 pyrazinamide Assoc w R - Interim
embB 4248003 p.Gln497Arg missense_variant 0.72 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
dnaA 698 p.Arg233Gln missense_variant 0.73 isoniazid 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 8040 p.Gly247Ser missense_variant 0.78 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 0.12 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
mshA 576488 p.Val381His missense_variant 0.17 isoniazid
ethionamide
rpoC 764931 p.Ala521Asp missense_variant 0.75 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.76 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 0.21 linezolid
fbiC 1303095 c.165G>A synonymous_variant 0.8 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1304962 p.Trp678Gly missense_variant 0.81 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rpsA 1834836 p.Met432Thr missense_variant 0.73 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 0.23 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 0.18 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.85 isoniazid Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.25 pyrazinamide Uncertain significance
PPE35 2170035 p.Val193Ala missense_variant 0.15 pyrazinamide Uncertain significance
PPE35 2170048 p.Leu189Val missense_variant 0.32 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.31 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518919 p.Gly269Ser missense_variant 0.68 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.73 para-aminosalicylic_acid
ribD 2986827 c.-12G>A upstream_gene_variant 0.84 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.72 para-aminosalicylic_acid
thyA 3073914 p.His186Gln missense_variant 0.21 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 0.23 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339741 c.624G>T synonymous_variant 0.2 pretomanid
delamanid
clofazimine
fbiD 3339744 c.627A>C synonymous_variant 0.21 pretomanid
delamanid
clofazimine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878567 c.-60C>G upstream_gene_variant 0.47 rifampicin
rpoA 3878578 c.-71C>A upstream_gene_variant 0.18 rifampicin Uncertain significance
rpoA 3878599 c.-92C>G upstream_gene_variant 0.27 rifampicin
rpoA 3878639 c.-132C>G upstream_gene_variant 0.13 rifampicin Uncertain significance
ddn 3987233 c.390C>T synonymous_variant 0.14 pretomanid
delamanid Not assoc w R - Interim
clpC1 4038287 c.2418C>T synonymous_variant 0.79 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.72 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.35 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.49 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.48 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.49 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.47 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.4 ethambutol Not assoc w R - Interim
embB 4249594 c.3081G>A synonymous_variant 0.31 ethambutol Not assoc w R - Interim
ethA 4328376 c.-903G>C upstream_gene_variant 0.18 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
gid 4408156 p.Leu16Arg missense_variant 0.84 streptomycin Not assoc w R