TB-Profiler result

Run: SRR28389884
Summary

Run ID: SRR28389884

Sample name:

Date: 2024-05-22T15:03:30.197698

Number of reads: 5150023

Percentage reads mapped: 99.48

Median coverage: 136.0

Strain: lineage2.2.1.2;lineage4.1.1.3

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
lineage2 East-Asian RD105 0.7
lineage4.1 Euro-American None 0.29
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.71
lineage4.1.1.3 Euro-American (X-type) RD193 0.33
lineage2.2 East-Asian (Beijing) RD105;RD207 0.69
lineage4 Euro-American None 0.33
lineage4.1.1 Euro-American (X-type) None 0.31
lineage2.2.1.2 East-Asian (Beijing) RD105;RD207;RD181;RD142 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.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid folC p.Glu40Gln 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.Asp94Ala missense_variant 0.17 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 761155 p.Ser450Leu missense_variant 0.32 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.35 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.28 isoniazid Assoc w R High-level resistance
folC 2747481 p.Glu40Gln missense_variant 0.3 para-aminosalicylic_acid 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
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 0.78 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.75 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.7 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.7 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.74 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.28 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.73 rifampicin Not assoc w R
rpoC 764766 p.Ala466Val missense_variant 0.24 rifampicin Uncertain significance
rpoC 764888 p.Leu507Val missense_variant 0.27 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.25 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 0.69 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.67 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.75 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.3 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.65 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302935 p.Pro2Arg missense_variant 0.68 clofazimine
pretomanid
delamanid
Rv1258c 1406760 c.580_581insC frameshift_variant 0.6 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 0.66 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 2154678 c.1434G>C synonymous_variant 0.28 isoniazid Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.74 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.6 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
ahpC 2726409 p.Asp73His missense_variant 0.29 isoniazid Uncertain significance
Rv2477c 2782447 c.1596C>T synonymous_variant 0.69 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin Not assoc w R - Interim
levofloxacin
kanamycin
rifampicin Not assoc w R - Interim
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449670 c.1167C>A synonymous_variant 0.31 ethionamide
whiB7 3568431 c.249C>G synonymous_variant 0.17 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.69 pyrazinamide 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 0.67 bedaquiline Uncertain significance
rifampicin Not assoc w R
panD 4044386 c.-105C>T upstream_gene_variant 0.31 pyrazinamide
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.33 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.72 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.33 ethambutol Not assoc w R
embB 4249678 c.3165C>A synonymous_variant 0.33 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.69 ethambutol Not assoc w R
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 0.69 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.69 streptomycin Not assoc w R