TB-Profiler result

Run: SRR6356970
Summary

Run ID: SRR6356970

Sample name:

Date: 2024-04-15T03:23:36.864337

Number of reads: 2711637

Percentage reads mapped: 99.52

Median coverage: 84.0

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 0.47
lineage4.1.2 Euro-American None 0.47
lineage4.2 Euro-American None 0.51
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.45
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) None 0.46
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ala286Val Uncertain significance Mutation from literature
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
c.22dupA Assoc w R High-level resistance
ethambutol embB p.Gly406Cys Assoc w R
pyrazinamide pncA p.Ala146Thr Assoc w R
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Thr500Asn Uncertain significance Mutation from literature
gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrB p.Thr500Asn Uncertain significance Mutation from literature
gyrA p.Asp94Gly 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.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA c.1261_1262dupCG 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
gyrB 6738 p.Thr500Asn missense_variant 0.15 moxifloxacin Uncertain significance Mutation from literature
levofloxacin Uncertain significance Mutation from literature
gyrA 7582 p.Asp94Gly missense_variant 0.14 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 760663 p.Ala286Val missense_variant 0.44 rifampicin Uncertain significance Mutation from literature
rpoB 761155 p.Ser450Leu missense_variant 0.56 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.49 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.93 capreomycin Assoc w R
amikacin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.52 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 0.5 isoniazid Assoc w R High-level resistance
katG 2156089 c.22dupA frameshift_variant 0.48 isoniazid Assoc w R High-level resistance
pncA 2288806 p.Ala146Thr missense_variant 0.54 pyrazinamide Assoc w R
embB 4247729 p.Gly406Cys missense_variant 0.38 ethambutol Assoc w R
ethA 4326211 c.1261_1262dupCG frameshift_variant 0.22 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
dnaA 1399 p.Gly467Arg missense_variant 0.35 isoniazid Uncertain significance
dnaA 1422 p.Met474Ile missense_variant 0.22 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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491247 c.465C>T synonymous_variant 0.44 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fgd1 491591 p.Lys270Met missense_variant 0.56 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.48 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 619969 p.Val27Ile missense_variant 0.64 capreomycin Not assoc w R - Interim
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.46 ethionamide Uncertain significance
rpoB 760106 c.300G>A synonymous_variant 0.51 rifampicin Not assoc w R
rpoB 760115 c.309C>T synonymous_variant 0.52 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.44 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 0.43 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.59 linezolid
Rv1129c 1254583 c.-49A>C upstream_gene_variant 0.55 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406584 p.Asp253Tyr missense_variant 0.51 streptomycin
isoniazid
pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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
bacA 2063685 c.1044G>A synonymous_variant 0.5 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2156484 c.-373A>C upstream_gene_variant 0.23 isoniazid Uncertain significance
katG 2156565 c.-455dupA upstream_gene_variant 0.21 isoniazid
PPE35 2169879 p.Phe245Cys missense_variant 0.61 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.5 isoniazid
eis 2715340 c.-8C>T upstream_gene_variant 0.47 amikacin Uncertain significance
kanamycin Uncertain significance
ribD 2986827 c.-12G>A upstream_gene_variant 0.49 para-aminosalicylic_acid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.14 capreomycin Uncertain significance
ald 3086742 c.-78A>C upstream_gene_variant 0.51 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3623222 c.1689A>G synonymous_variant 0.51 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.42 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 0.38 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.43 ethambutol Not assoc w R - Interim
aftB 4267274 c.1563G>A synonymous_variant 0.39 ethambutol
ubiA 4269148 p.Val229Ala missense_variant 0.12 ethambutol Uncertain significance
ubiA 4269731 p.Ala35Thr missense_variant 0.28 ethambutol Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.47 ethionamide
whiB6 4338513 c.9C>T synonymous_variant 0.53 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin