TB-Profiler result

Run: SRR28351408
Summary

Run ID: SRR28351408

Sample name:

Date: 2024-05-22T17:27:56.324595

Number of reads: 1341853

Percentage reads mapped: 99.86

Median coverage: 42.0

Strain: lineage2.2.1;lineage4

Spoligotype:

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.92
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.95
lineage2.2 East-Asian (Beijing) RD105;RD207 0.94
lineage4 Euro-American None 0.06
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
p.Glu761Asp Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Asp354Ala Assoc w R
pyrazinamide pncA p.Leu116Arg Assoc w R - Interim
streptomycin rrs n.517C>T 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
capreomycin
kanamycin eis c.-37G>T Assoc w R
cycloserine
ethionamide ethA c.-7T>C Assoc w R - Interim
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 7570 p.Ala90Val missense_variant 0.85 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpoB 762089 p.Glu761Asp missense_variant 0.68 rifampicin Uncertain significance Mutation from literature
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.63 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.85 isoniazid Assoc w R High-level resistance
pncA 2288895 p.Leu116Arg missense_variant 0.72 pyrazinamide Assoc w R - Interim
eis 2715369 c.-37G>T upstream_gene_variant 0.8 kanamycin Assoc w R
embB 4247574 p.Asp354Ala missense_variant 0.86 ethambutol Assoc w R
ethA 4327480 c.-7T>C upstream_gene_variant 0.78 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 491742 c.960T>C synonymous_variant 0.97 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.87 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.89 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.93 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.95 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.92 rifampicin Not assoc w R
rpoC 766645 p.Glu1092Asp missense_variant 0.93 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 0.97 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.85 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.96 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.89 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 0.85 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.96 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476300 n.2643G>A non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476393 n.2736C>T non_coding_transcript_exon_variant 0.46 capreomycin
linezolid
rpsA 1833949 c.408T>C synonymous_variant 0.94 pyrazinamide
rpsA 1833961 c.420C>G synonymous_variant 0.95 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.96 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.96 pyrazinamide
rpsA 1833985 c.444G>C synonymous_variant 0.96 pyrazinamide
rpsA 1833988 c.447C>G synonymous_variant 0.96 pyrazinamide
rpsA 1833991 c.450C>A synonymous_variant 0.96 pyrazinamide
rpsA 1833997 c.456G>C synonymous_variant 0.96 pyrazinamide
rpsA 1834009 c.468C>T synonymous_variant 0.96 pyrazinamide
rpsA 1834012 c.471G>T synonymous_variant 0.96 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.96 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.96 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.95 pyrazinamide
rpsA 1834069 c.528G>C synonymous_variant 0.93 pyrazinamide
rpsA 1834093 c.552G>C synonymous_variant 0.92 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.92 pyrazinamide
rpsA 1834105 c.564C>T synonymous_variant 0.9 pyrazinamide
rpsA 1834108 c.567C>A synonymous_variant 0.89 pyrazinamide
rpsA 1834114 c.573G>C synonymous_variant 0.87 pyrazinamide
rpsA 1834135 c.594G>C synonymous_variant 0.74 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.9 pyrazinamide Not assoc w R - Interim
rpsA 1834690 c.1149T>C synonymous_variant 0.41 pyrazinamide
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
tlyA 1918037 p.Arg33Pro missense_variant 0.63 capreomycin
katG 2154724 p.Arg463Leu missense_variant 0.92 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.96 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.88 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.97 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.95 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.91 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269148 p.Val229Ala missense_variant 0.77 ethambutol Uncertain significance
ethA 4326632 p.His281Pro missense_variant 0.17 ethionamide Uncertain significance
whiB6 4338563 c.-42G>T upstream_gene_variant 0.63 capreomycin Not assoc w R
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 0.98 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.88 streptomycin Not assoc w R