TB-Profiler result

Run: SAMN02419670
Summary

Run ID: SAMN02419670

Sample name:

Date: 2024-10-04T18:02:27.025356

Number of reads: 14041815

Percentage reads mapped: 99.43

Median coverage: 333.0

Strain: lineage2.2.1;lineage4.3.3

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
lineage4.3 Euro-American (LAM) None 0.19
lineage2 East-Asian RD105 0.82
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.82
lineage2.2 East-Asian (Beijing) RD105;RD207 0.82
lineage4 Euro-American None 0.21
lineage4.3.3 Euro-American (LAM) RD115 0.18
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)
p.Ser94Ala Assoc w R - Interim 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.Met306Ile Assoc w R
p.Tyr319Ser Assoc w R
pyrazinamide pncA c.-7T>C Assoc w R - Interim
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.514A>C Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Gly88Cys Assoc w R High-level resistance
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Gly88Cys Assoc w R
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
eis c.-8C>A Uncertain significance Mutation from literature
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
p.Ser94Ala Assoc w R - Interim
ethA p.Gly385Asp Uncertain significance Mutation from literature
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 7563 p.Gly88Cys missense_variant 0.19 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
gyrA 7582 p.Asp94Gly missense_variant 0.82 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.79 streptomycin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.21 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.97 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.23 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)
inhA 1674481 p.Ser94Ala missense_variant 0.21 ethionamide Assoc w R - Interim
isoniazid Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289248 c.-7T>C upstream_gene_variant 0.17 pyrazinamide Assoc w R - Interim
eis 2715340 c.-8C>A upstream_gene_variant 0.15 kanamycin Uncertain significance Mutation from literature
folC 2747480 p.Glu40Gly missense_variant 0.77 para-aminosalicylic_acid Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.77 ethambutol Assoc w R
embB 4247469 p.Tyr319Ser missense_variant 0.22 ethambutol Assoc w R
ethA 4326320 p.Gly385Asp missense_variant 0.83 ethionamide Uncertain significance Mutation from literature
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 0.19 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 0.22 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
Rv0010c 13629 c.-71T>G upstream_gene_variant 0.82 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.81 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.79 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.8 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 656837 p.Ser212Pro missense_variant 0.58 ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.82 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.8 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.83 rifampicin Not assoc w R
rpoC 764918 p.Val517Leu missense_variant 0.84 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.2 rifampicin Not assoc w R
rpoC 766487 p.Pro1040Thr missense_variant 0.19 rifampicin Uncertain significance
rpoC 767007 p.Ala1213Glu missense_variant 0.83 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.77 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.8 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.81 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254126 p.Tyr137Asp missense_variant 0.77 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.8 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303095 c.165G>A synonymous_variant 0.17 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1304962 p.Trp678Gly missense_variant 0.19 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.81 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.77 pyrazinamide Not assoc w R - Interim
rpsA 1834429 c.888C>T synonymous_variant 0.81 pyrazinamide
rpsA 1834836 p.Met432Thr missense_variant 0.15 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 0.8 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.21 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.81 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2288790 p.Leu151Trp missense_variant 0.83 pyrazinamide Uncertain significance
kasA 2518919 p.Gly269Ser missense_variant 0.21 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.23 para-aminosalicylic_acid
ribD 2986827 c.-12G>A upstream_gene_variant 0.14 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.15 para-aminosalicylic_acid
ald 3086731 c.-89A>G upstream_gene_variant 0.79 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.84 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.8 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.19 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243346 c.114A>G synonymous_variant 0.81 ethambutol Not assoc w R - Interim
embA 4243460 c.228C>T synonymous_variant 0.8 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.77 ethambutol Not assoc w R
whiB6 4338371 p.Thr51Pro missense_variant 0.8 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
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 4407588 c.615A>G synonymous_variant 0.82 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.83 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.14 streptomycin Not assoc w R