TB-Profiler result

Run: ERR4796358
Summary

Run ID: ERR4796358

Sample name:

Date: 2024-10-05T05:43:39.085709

Number of reads: 3920574

Percentage reads mapped: 99.7

Median coverage: 105.0

Strain: lineage3.1.2;lineage4.1.1.1

Spoligotype:

Drug-resistance: Other

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.75
lineage3.1.2 East-African-Indian RD750 0.77
lineage4.1 Euro-American None 0.24
lineage4.1.1.1 Euro-American (X-type) RD183 0.26
lineage4 Euro-American None 0.29
lineage4.1.1 Euro-American (X-type) None 0.3
lineage3.1 East-African-Indian RD750 0.69
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly 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 7582 p.Asp94Gly missense_variant 0.23 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
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 8864 c.1563C>T synonymous_variant 0.2 levofloxacin
moxifloxacin
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 0.75 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.81 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.22 ethionamide Uncertain significance
mmaA3 738280 c.-131G>A upstream_gene_variant 0.24 isoniazid
rpoB 759746 c.-61C>T upstream_gene_variant 0.72 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.72 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.7 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.29 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 0.66 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777313 p.Pro390Thr missense_variant 0.33 bedaquiline
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.29 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.76 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1853629 c.24G>A synonymous_variant 0.15 linezolid 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 0.77 capreomycin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.81 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.79 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.71 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 0.73 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.65 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.9 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.77 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3449379 c.876G>A synonymous_variant 0.3 ethionamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641447 p.Thr302Met missense_variant 0.14 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
alr 3840864 p.Asp186Gly missense_variant 0.2 cycloserine
rpoA 3877553 p.Glu319Lys missense_variant 0.34 rifampicin Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.74 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.65 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240390 p.Asn176Lys missense_variant 0.27 ethambutol Uncertain significance
embC 4240897 c.1035C>G synonymous_variant 0.3 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.79 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.31 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.2 ethambutol Not assoc w R
ethA 4327161 p.Ile105Leu missense_variant 0.25 ethionamide Uncertain significance
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 4407551 p.Met218Val missense_variant 0.26 streptomycin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 0.73 streptomycin Not assoc w R