TB-Profiler result

Run: SRR7755720

Summary

Run ID: SRR7755720

Sample name:

Date: 2024-03-25T22:18:19.634881

Number of reads: 8291217

Percentage reads mapped: 99.11

Median coverage: 158.0

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 0.36
lineage4.2 Euro-American None 0.63
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.36
lineage2.2 East-Asian (Beijing) RD105;RD207 0.37
lineage4 Euro-American None 0.66
lineage4.2.1 Euro-American (TUR) None 0.65
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asn Assoc w R
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.Ser297Ala Uncertain significance Mutation from literature
pyrazinamide pncA p.Cys14Tyr Uncertain significance Mutation from literature
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val 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.-12C>T 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 7570 p.Ala90Val missense_variant 0.67 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761139 p.His445Asn missense_variant 0.22 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.76 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.39 streptomycin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.64 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.14 kanamycin Assoc w R
capreomycin Assoc w R
amikacin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.66 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 2289201 p.Cys14Tyr missense_variant 0.69 pyrazinamide Uncertain significance Mutation from literature
eis 2715344 c.-12C>T upstream_gene_variant 0.69 kanamycin Assoc w R
thyX 3067961 c.-16C>T upstream_gene_variant 0.4 para-aminosalicylic_acid Mutation from literature
thyA 3073808 p.Arg222Gly missense_variant 0.46 para-aminosalicylic_acid Mutation from literature
embB 4247402 p.Ser297Ala missense_variant 0.67 ethambutol Uncertain significance Mutation from literature
ethA 4326339 p.Asn379Asp missense_variant 0.32 ethionamide Assoc w R - Interim
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 0.65 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.34 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.33 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 619969 p.Val27Ile missense_variant 0.7 capreomycin Not assoc w R - Interim
amikacin Not assoc w R
kanamycin Uncertain significance
ccsA 620625 p.Ile245Met missense_variant 0.26 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 0.37 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.32 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.68 rifampicin Uncertain significance
rpoC 766645 p.Glu1092Asp missense_variant 0.34 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 0.4 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.4 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.37 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.62 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.33 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364706 c.294G>A synonymous_variant 0.34 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.3 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 0.33 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 0.69 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 0.63 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.34 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.35 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.62 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086742 c.-78A>C upstream_gene_variant 0.61 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568579 c.100dupG frameshift_variant 0.14 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB7 3568893 c.-215delC upstream_gene_variant 0.25 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.38 pyrazinamide Not assoc w R - Interim
lpqB 3623222 c.1689A>G synonymous_variant 0.66 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
mtrB 3626562 p.Pro18Ser missense_variant 0.33 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640675 p.Val45Ile missense_variant 0.7 clofazimine
pretomanid
delamanid
fbiB 3641810 c.276G>C synonymous_variant 0.33 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
alr 3840391 p.Asp344Asn missense_variant 0.64 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.37 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.61 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.19 ethambutol Not assoc w R
ethA 4326632 p.His281Pro missense_variant 0.68 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.68 ethionamide
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 0.32 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.38 streptomycin Not assoc w R