TB-Profiler result

Run: ERR4799919
Summary

Run ID: ERR4799919

Sample name:

Date: 2024-04-15T04:33:14.973988

Number of reads: 3540788

Percentage reads mapped: 99.55

Median coverage: 86.0

Strain: lineage3.1.2;lineage4.2.2.2

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
lineage4.2.2 Euro-American (Ural) None 0.44
lineage3 East-African-Indian RD750 0.5
lineage3.1.2 East-African-Indian RD750 0.48
lineage4.2 Euro-American None 0.5
lineage4 Euro-American None 0.49
lineage4.2.2.2 Euro-American (Ural) None 0.45
lineage3.1 East-African-Indian RD750 0.52
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 katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gly406Ala Assoc w R
pyrazinamide pncA c.86delG Assoc w R
streptomycin rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Asn Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Tyr143* Assoc w R
clofazimine
para-aminosalicylic_acid folC p.Glu40Gly Mutation from literature
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 7581 p.Asp94Asn missense_variant 0.55 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.56 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.38 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.63 isoniazid Assoc w R High-level resistance
pncA 2289155 c.86delG frameshift_variant 0.53 pyrazinamide Assoc w R
folC 2747480 p.Glu40Gly missense_variant 0.52 para-aminosalicylic_acid Mutation from literature
embB 4247730 p.Gly406Ala missense_variant 0.43 ethambutol Assoc w R
ethA 4327045 p.Tyr143* stop_gained 0.45 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 429 p.Asn143Lys missense_variant 0.47 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7481 c.180C>T synonymous_variant 0.52 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8688 p.Ala463Ser missense_variant 0.44 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 491742 c.960T>C synonymous_variant 0.46 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576077 c.730C>T synonymous_variant 0.41 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.55 ethionamide Not assoc w R - Interim
Rv0565c 657425 p.Gly16Ser missense_variant 0.52 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.39 rifampicin Not assoc w R
rpoB 761489 c.1683G>A synonymous_variant 0.37 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.54 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.5 rifampicin Not assoc w R
rpoC 763923 p.Glu185Val missense_variant 0.49 rifampicin
rpoC 767123 p.Val1252Met missense_variant 0.41 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.49 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776585 c.1896C>T synonymous_variant 0.53 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.4 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.51 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406242 p.Ala367Thr missense_variant 0.49 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
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
tlyA 1918104 c.165G>A synonymous_variant 0.44 capreomycin Not assoc w R - Interim
bacA 2063685 c.1044G>A synonymous_variant 0.61 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 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.47 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.52 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.58 pyrazinamide Not assoc w R
PPE35 2169634 p.Ala327Thr missense_variant 0.54 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.53 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.6 pyrazinamide
eis 2714888 p.Phe149Val missense_variant 0.43 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726105 c.-88G>A upstream_gene_variant 0.47 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.55 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.34 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
ald 3086742 c.-78A>C upstream_gene_variant 0.69 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449404 c.902_904dupCCA disruptive_inframe_insertion 0.43 ethionamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.46 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.53 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240327 c.465G>A synonymous_variant 0.48 ethambutol Not assoc w R - Interim
embC 4242075 p.Arg738Gln missense_variant 0.56 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269721 p.Ala38Val missense_variant 0.47 ethambutol Uncertain significance
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
whiB6 4338917 c.-396C>A upstream_gene_variant 0.5 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.44 streptomycin Not assoc w R
gid 4408273 c.-71C>T upstream_gene_variant 0.43 streptomycin Uncertain significance