TB-Profiler result

Run: ERR2706966
Summary

Run ID: ERR2706966

Sample name:

Date: 2024-04-15T18:38:31.138495

Number of reads: 4019803

Percentage reads mapped: 99.58

Median coverage: 113.0

Strain: lineage4.3.3;lineage4.6.1.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.44
lineage4.6 Euro-American None 0.59
lineage4.6.1.2 Euro-American RD724 0.57
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.43
lineage4.6.1 Euro-American (Uganda) RD724 0.55
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Trp Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.His51Tyr Assoc w R
streptomycin rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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
rpoB 761155 p.Ser450Trp missense_variant 0.12 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.15 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.14 isoniazid Assoc w R High-level resistance
pncA 2289091 p.His51Tyr missense_variant 0.2 pyrazinamide 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
gyrB 5723 p.Ala162Ser missense_variant 0.32 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7539 p.Thr80Ala missense_variant 0.72 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
gyrA 7570 p.Ala90Gly missense_variant 0.69 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.47 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
mshA 575240 c.-108G>A upstream_gene_variant 0.22 ethionamide Uncertain significance
isoniazid Uncertain significance
rpoC 764810 p.Pro481Thr missense_variant 0.42 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.45 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
fbiC 1304608 p.Thr560Ala missense_variant 0.17 clofazimine
pretomanid
delamanid
embR 1416410 p.Leu313Arg missense_variant 0.55 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1475373 n.1716G>A non_coding_transcript_exon_variant 0.63 capreomycin Uncertain significance
linezolid
fabG1 1673277 c.-163_-162insT upstream_gene_variant 0.17 ethionamide
isoniazid
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.46 isoniazid
eis 2715432 c.-100C>T upstream_gene_variant 0.13 amikacin
kanamycin
Rv2477c 2783992 c.51T>C synonymous_variant 0.3 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin
Rv2477c 2784137 c.-95C>G upstream_gene_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ribD 2987533 p.Gly232Ala missense_variant 0.15 para-aminosalicylic_acid
Rv2681 2996876 c.138A>C synonymous_variant 0.53 capreomycin Not assoc w R
Rv2752c 3065920 p.Pro91Leu missense_variant 0.57 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.28 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.4 cycloserine
Rv3083 3449301 c.798G>A synonymous_variant 0.2 ethionamide Not assoc w R - Interim
whiB7 3569029 c.-350A>G upstream_gene_variant 0.67 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Not assoc w R
lpqB 3624748 p.Phe55Leu missense_variant 0.36 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.42 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627602 c.-253C>G upstream_gene_variant 0.14 bedaquiline Uncertain significance
rifampicin Uncertain significance
ddn 3987215 c.372A>G synonymous_variant 0.58 delamanid
pretomanid
clpC1 4038287 c.2418C>T synonymous_variant 0.45 pyrazinamide Not assoc w R
glpK 4139670 p.Cys29Tyr missense_variant 0.56 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Not assoc w R
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242182 p.Ala774Ser missense_variant 0.28 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245055 p.Thr608Asn missense_variant 0.65 ethambutol Uncertain significance
embB 4247209 c.696A>G synonymous_variant 0.12 ethambutol Not assoc w R - Interim
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 4407926 p.Pro93Ser missense_variant 0.16 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.37 streptomycin Not assoc w R