TB-Profiler result

Run: ERR4799994
Summary

Run ID: ERR4799994

Sample name:

Date: 2024-04-16T02:28:23.119991

Number of reads: 4595950

Percentage reads mapped: 99.58

Median coverage: 120.0

Strain: lineage3.1.2;lineage4.3.3

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
lineage3 East-African-Indian RD750 0.39
lineage4.3 Euro-American (LAM) None 0.55
lineage3.1.2 East-African-Indian RD750 0.41
lineage4 Euro-American None 0.57
lineage4.3.3 Euro-American (LAM) RD115 0.54
lineage3.1 East-African-Indian RD750 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.Ser450Trp Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide pncA c.521_522insT Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Asn Assoc w R
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
gyrA 7581 p.Asp94Asn missense_variant 0.39 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Trp missense_variant 0.44 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.45 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.49 isoniazid Assoc w R High-level resistance
pncA 2288720 c.521_522insT frameshift_variant 0.43 pyrazinamide Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.4 ethambutol 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
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 8040 p.Gly247Ser missense_variant 0.54 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9758 c.2457C>T synonymous_variant 0.43 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13605 c.-47G>T upstream_gene_variant 0.42 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.55 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620079 c.189C>T synonymous_variant 0.37 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
Rv0565c 657081 c.390G>A synonymous_variant 0.45 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 0.44 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.33 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.35 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.55 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 0.35 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 0.99 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.42 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 0.63 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
tlyA 1918104 c.165G>A synonymous_variant 0.41 capreomycin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.41 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.55 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.48 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.51 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
pncA 2289047 c.195C>T synonymous_variant 0.38 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.43 pyrazinamide
kasA 2518919 p.Gly269Ser missense_variant 0.67 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.54 isoniazid Not assoc w R
folC 2746340 p.Ala420Val missense_variant 0.58 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.41 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.58 para-aminosalicylic_acid
thyA 3074247 p.His75Gln missense_variant 0.32 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.47 pyrazinamide Not assoc w R
clpC1 4040675 c.30C>G synonymous_variant 0.37 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.33 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.42 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.49 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.99 ethambutol Not assoc w R
ethA 4327229 p.Leu82Arg missense_variant 0.65 ethionamide 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 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.42 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.54 streptomycin Not assoc w R