TB-Profiler result

Run: SRR14802167
Summary

Run ID: SRR14802167

Sample name:

Date: 2024-10-05T13:03:16.600546

Number of reads: 3600265

Percentage reads mapped: 99.57

Median coverage: 118.0

Strain: lineage2.2.1;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
lineage2 East-Asian RD105 0.69
lineage4.2 Euro-American None 0.3
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.69
lineage2.2 East-Asian (Beijing) RD105;RD207 0.69
lineage4 Euro-American None 0.31
lineage4.2.1 Euro-American (TUR) None 0.32
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)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Lys96Glu Assoc w R
p.His57Asp Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
gid c.193dupG 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 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 p.Asn379Asp Assoc w R - Interim
clofazimine
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
thyA p.Arg222Gly 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 7582 p.Asp94Gly missense_variant 0.44 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.67 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.76 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.44 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.34 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)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288956 p.Lys96Glu missense_variant 0.49 pyrazinamide Assoc w R
pncA 2289073 p.His57Asp missense_variant 0.22 pyrazinamide Assoc w R
thyX 3067961 c.-16C>T upstream_gene_variant 0.7 para-aminosalicylic_acid Mutation from literature
thyA 3073808 p.Arg222Gly missense_variant 0.69 para-aminosalicylic_acid Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.7 ethambutol Assoc w R
ethA 4326339 p.Asn379Asp missense_variant 0.75 ethionamide Assoc w R - Interim
gid 4408009 c.193dupG frameshift_variant 0.24 streptomycin 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 0.28 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.67 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.74 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.71 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.7 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.65 ethionamide Uncertain significance
nusG 734817 c.564C>T synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.72 rifampicin Not assoc w R
rpoC 764651 p.Ser428Ala missense_variant 0.71 rifampicin Uncertain significance
rpoC 766645 p.Glu1092Asp missense_variant 0.69 rifampicin Not assoc w R
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 0.62 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.62 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.69 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.27 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.71 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.68 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.68 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1407423 c.-83G>A upstream_gene_variant 0.35 streptomycin
pyrazinamide
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.67 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
bacA 2063685 c.1044G>A synonymous_variant 0.34 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.4 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.66 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.75 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.32 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ribD 2986827 c.-12G>A upstream_gene_variant 0.27 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 0.37 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087067 c.250dupC frameshift_variant 0.32 cycloserine
Rv3083 3449173 p.Asp224Asn missense_variant 0.33 ethionamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.71 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 0.71 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3641810 c.276G>C synonymous_variant 0.66 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
alr 3841509 c.-89A>G upstream_gene_variant 0.25 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.77 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.36 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.67 ethambutol Not assoc w R
ethA 4328376 c.-903G>C upstream_gene_variant 0.23 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
gid 4407588 c.615A>G synonymous_variant 0.73 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.74 streptomycin Not assoc w R