TB-Profiler result

Run: SRR10525342
Summary

Run ID: SRR10525342

Sample name:

Date: 2024-10-03T20:26:34.469673

Number of reads: 1691347

Percentage reads mapped: 98.39

Median coverage: 50.0

Strain: lineage4.1.2.1;lineage4.2.1

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
lineage4.1 Euro-American None 0.79
lineage4.1.2 Euro-American None 0.75
lineage4.2 Euro-American None 0.19
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.74
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) None 0.25
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.-154G>A Assoc w R Alias fabG1_p.Leu203Leu. 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.Gln497Lys Assoc w R
pyrazinamide pncA p.Lys96Thr Assoc w R
streptomycin rpsL p.Lys88Arg 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)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide inhA c.-154G>A Assoc w R - Interim Alias fabG1_p.Leu203Leu
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 0.24 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 0.36 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.23 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.16 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.39 ethionamide Assoc w R - Interim Alias fabG1_p.Leu203Leu
isoniazid Assoc w R Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.21 isoniazid Assoc w R High-level resistance
pncA 2288955 p.Lys96Thr missense_variant 0.27 pyrazinamide Assoc w R
embB 4248002 p.Gln497Lys missense_variant 0.27 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
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 0.16 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fgd1 491591 p.Lys270Met missense_variant 0.77 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.74 isoniazid Not assoc w R
ethionamide Not assoc w R
mshA 576513 p.Leu389Pro missense_variant 0.31 isoniazid Uncertain significance
ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.72 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.79 rifampicin Not assoc w R
rpoB 761267 c.1461C>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoB 761407 p.Val534Ala missense_variant 0.3 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.87 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 0.24 linezolid
sigE 1364358 c.-55C>T upstream_gene_variant 0.27 pyrazinamide
embR 1416607 c.741G>A synonymous_variant 0.56 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673359 c.-843T>C upstream_gene_variant 0.11 isoniazid
ethionamide
inhA 1673361 c.-841C>G upstream_gene_variant 0.11 isoniazid
ethionamide
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 0.35 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.14 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 0.69 isoniazid
ribD 2986827 c.-12G>A upstream_gene_variant 0.27 para-aminosalicylic_acid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.12 capreomycin Uncertain significance
Rv2680 2996083 c.-22C>A upstream_gene_variant 0.14 capreomycin
Rv2681 2997736 c.1009_1011delCCG conservative_inframe_deletion 0.79 capreomycin Uncertain significance
ald 3086742 c.-78A>C upstream_gene_variant 0.3 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3623222 c.1689A>G synonymous_variant 0.2 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 0.8 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 0.77 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.29 ethambutol Not assoc w R - Interim
ubiA 4269391 p.Val148Ala missense_variant 0.22 ethambutol Uncertain significance
ethA 4327088 p.Leu129Arg missense_variant 0.17 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.32 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
whiB6 4338787 c.-266G>A upstream_gene_variant 0.64 kanamycin
capreomycin
amikacin