TB-Profiler result

Run: ERR4797417
Summary

Run ID: ERR4797417

Sample name:

Date: 2024-04-15T16:20:49.692496

Number of reads: 3735416

Percentage reads mapped: 99.55

Median coverage: 110.0

Strain: lineage2.2.1.1;lineage4.1.1.1

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
lineage2 East-Asian RD105 0.28
lineage4.1 Euro-American None 0.75
lineage4.1.1.1 Euro-American (X-type) RD183 0.7
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.26
lineage2.2 East-Asian (Beijing) RD105;RD207 0.22
lineage4 Euro-American None 0.73
lineage4.1.1 Euro-American (X-type) None 0.76
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.23
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.Met306Val Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.1242delT Assoc w R
c.754_755dupGC 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
gyrA 7582 p.Asp94Gly missense_variant 0.22 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.23 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.27 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.34 isoniazid Assoc w R High-level resistance
embB 4247429 p.Met306Val missense_variant 0.37 ethambutol Assoc w R
ethA 4326231 c.1242delT frameshift_variant 0.2 ethionamide Assoc w R
ethA 4326718 c.754_755dupGC frameshift_variant 0.12 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 5936 p.Ala233Pro missense_variant 0.1 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 491742 c.960T>C synonymous_variant 0.23 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.24 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.22 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.31 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.33 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.51 ethionamide Uncertain significance
rpoB 761292 p.Val496Met missense_variant 0.13 rifampicin Uncertain significance
rpoC 764363 p.Gly332Ser missense_variant 0.13 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.78 rifampicin Not assoc w R
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 0.25 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.25 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.27 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.76 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.26 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.24 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.27 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
katG 2154724 p.Arg463Leu missense_variant 0.28 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.25 pyrazinamide Not assoc w R
PPE35 2167967 c.2645dupC frameshift_variant 0.76 pyrazinamide Uncertain significance
PPE35 2168034 p.Thr860Ile missense_variant 0.74 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2714846 p.Val163Ile missense_variant 0.24 amikacin Not assoc w R
kanamycin Not assoc w R
Rv2477c 2782877 p.Val389Ala missense_variant 0.69 ethambutol
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
thyA 3074282 p.Arg64Cys missense_variant 0.18 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.9 cycloserine
ald 3087711 p.Val298Met missense_variant 0.17 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.22 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.19 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3641238 c.696G>A synonymous_variant 0.66 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiA 3641447 p.Thr302Met missense_variant 0.77 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
rpoA 3877553 p.Glu319Lys missense_variant 0.67 rifampicin Not assoc w R
embC 4239656 c.-207C>T upstream_gene_variant 0.77 ethambutol Uncertain significance
embC 4240897 c.1035C>G synonymous_variant 0.79 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 0.68 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.17 ethambutol Not assoc w R
embB 4246746 p.Asp78Gly missense_variant 0.74 ethambutol Uncertain significance
embB 4247880 p.Val456Ala missense_variant 0.29 ethambutol Uncertain significance
embB 4248115 c.1602C>T synonymous_variant 0.4 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.76 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.14 ethambutol Not assoc w R
ubiA 4269245 p.His197Tyr missense_variant 0.73 ethambutol
whiB6 4338410 p.Pro38Ala missense_variant 0.16 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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
gid 4407588 c.615A>G synonymous_variant 0.17 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.26 streptomycin Not assoc w R
gid 4408266 c.-64C>G upstream_gene_variant 0.1 streptomycin