TB-Profiler result

Run: SRR7755683
Summary

Run ID: SRR7755683

Sample name:

Date: 2024-10-04T17:06:18.359685

Number of reads: 7041710

Percentage reads mapped: 90.79

Median coverage: 133.0

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 0.67
lineage4.2 Euro-American None 0.36
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.65
lineage2.2 East-Asian (Beijing) RD105;RD207 0.7
lineage4 Euro-American None 0.34
lineage4.2.1 Euro-American (TUR) None 0.35
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
rrs n.888G>A Uncertain significance Mutation from literature
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
eis c.-14C>T Assoc w R - Interim Can only confer resistance if genetically linked to a functional Eis
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
eis c.-12C>T Assoc w R
c.-14C>T Assoc w R Can only confer resistance if genetically linked to a functional Eis
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 0.26 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761139 p.His445Asn missense_variant 0.6 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.41 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.67 streptomycin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.43 streptomycin Assoc w R
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance Mutation from literature
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.25 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.32 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 0.36 pyrazinamide Uncertain significance Mutation from literature
eis 2715344 c.-12C>T upstream_gene_variant 0.28 kanamycin Assoc w R
eis 2715346 c.-14C>T upstream_gene_variant 0.25 amikacin Assoc w R - Interim Can only confer resistance if genetically linked to a functional Eis
kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
thyX 3067961 c.-16C>T upstream_gene_variant 0.73 para-aminosalicylic_acid Mutation from literature
thyA 3073808 p.Arg222Gly missense_variant 0.81 para-aminosalicylic_acid Mutation from literature
embB 4247402 p.Ser297Ala missense_variant 0.32 ethambutol Uncertain significance Mutation from literature
ethA 4326339 p.Asn379Asp missense_variant 0.61 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 0.35 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fgd1 491742 c.960T>C synonymous_variant 0.7 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.56 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 619969 p.Val27Ile missense_variant 0.37 kanamycin Uncertain significance
capreomycin Not assoc w R - Interim
amikacin Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.72 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.64 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.61 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.66 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.28 rifampicin Uncertain significance
rpoC 766645 p.Glu1092Asp missense_variant 0.61 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 0.68 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.71 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.57 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 0.34 linezolid
Rv1129c 1254056 p.Asp160Ala missense_variant 0.18 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.65 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 0.72 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.61 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.1 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.13 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.12 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.33 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.17 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.55 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 0.35 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 0.39 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.63 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.71 pyrazinamide Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.35 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
ald 3086742 c.-78A>C upstream_gene_variant 0.31 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568893 c.-215delC upstream_gene_variant 0.21 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.69 pyrazinamide Not assoc w R - Interim
lpqB 3623222 c.1689A>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
bedaquiline 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 0.55 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3640675 p.Val45Ile missense_variant 0.37 pretomanid
delamanid
clofazimine
fbiB 3641810 c.276G>C synonymous_variant 0.5 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
alr 3840391 p.Asp344Asn missense_variant 0.37 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.73 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.3 ethambutol Not assoc w R - Interim
aftB 4267331 c.1506C>A synonymous_variant 0.19 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.68 ethambutol Not assoc w R
ethA 4326632 p.His281Pro missense_variant 0.27 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.41 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 0.7 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.64 streptomycin Not assoc w R