TB-Profiler result

Run: ERR176616
Summary

Run ID: ERR176616

Sample name:

Date: 2024-10-05T12:28:00.791445

Number of reads: 2805483

Percentage reads mapped: 99.6

Median coverage: 64.0

Strain: lineage1.1.3.2;lineage4.3.4.2.1

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 0.61
lineage1.1.3 Indo-Oceanic RD239 0.39
lineage1.1.3.2 Indo-Oceanic RD239 0.35
lineage1.1 Indo-Oceanic RD239 0.34
lineage4 Euro-American None 0.65
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.6
lineage1 Indo-Oceanic RD239 0.37
lineage4.3.4 Euro-American (LAM) RD174 0.63
lineage4.3.4.2 Euro-American (LAM) RD174 0.64
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 embA c.-16C>T Uncertain significance Mutation from literature
pyrazinamide pncA p.Gln141Pro Assoc w R
streptomycin rrs n.513C>T Uncertain significance Mutation from literature
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.Ser450Leu missense_variant 0.58 rifampicin Assoc w R
rrs 1472358 n.513C>T non_coding_transcript_exon_variant 0.76 streptomycin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.69 isoniazid Assoc w R High-level resistance
pncA 2288820 p.Gln141Pro missense_variant 0.66 pyrazinamide Assoc w R
embA 4243217 c.-16C>T upstream_gene_variant 0.62 ethambutol Uncertain significance 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
dnaA 1215 p.Asp405Glu missense_variant 0.51 isoniazid Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.45 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6140 p.Val301Leu missense_variant 0.56 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8188 p.Leu296Pro missense_variant 0.37 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8452 p.Ala384Val missense_variant 0.43 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.39 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
Rv0010c 13298 p.Ile87Met missense_variant 0.35 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.39 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 619695 c.-196G>A upstream_gene_variant 0.45 kanamycin
capreomycin
amikacin
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.31 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.32 rifampicin Not assoc w R
rpoB 762714 p.Val970Met missense_variant 0.64 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.27 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.38 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.4 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.62 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.34 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.37 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 0.31 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.25 linezolid Not assoc w R
rplC 801166 p.Gly120Ser missense_variant 0.43 linezolid Uncertain significance
Rv1129c 1254189 p.Val116Phe missense_variant 0.69 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.3 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1129c 1254580 c.-46C>G upstream_gene_variant 0.69 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.3 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.4 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.38 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1674883 p.Ile228Val missense_variant 0.36 isoniazid Uncertain significance
ethionamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.38 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.29 linezolid Not assoc w R
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
bacA 2062922 p.Ile603Val missense_variant 0.37 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2064420 c.309C>T synonymous_variant 0.43 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.33 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.35 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.32 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.35 bedaquiline Not assoc w R - Interim
clofazimine 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
kasA 2518132 c.18C>T synonymous_variant 0.39 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.3 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 0.35 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
thyA 3073868 p.Thr202Ala missense_variant 0.67 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.39 ethionamide Uncertain significance
Rv3236c 3612009 p.Ala370Thr missense_variant 0.54 pyrazinamide Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.53 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3642173 c.639G>A synonymous_variant 0.36 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
alr 3840719 c.702A>G synonymous_variant 0.67 cycloserine
rpoA 3878687 c.-180A>C upstream_gene_variant 0.31 rifampicin Uncertain significance
clpC1 4038287 c.2418C>T synonymous_variant 0.64 pyrazinamide Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.42 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.39 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.4 ethambutol Not assoc w R
embC 4241539 c.1677T>C synonymous_variant 0.56 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.46 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.34 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.48 ethambutol Not assoc w R
embB 4248730 c.2217C>T synonymous_variant 0.46 ethambutol
ubiA 4269387 p.Glu149Asp missense_variant 0.35 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.4 ethambutol Not assoc w R
ethA 4327229 p.Leu82Pro missense_variant 0.64 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 4338603 c.-82C>T upstream_gene_variant 0.4 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 4407588 c.615A>G synonymous_variant 0.34 streptomycin Not assoc w R
gid 4407780 c.423G>A synonymous_variant 0.25 streptomycin Not assoc w R - Interim
gid 4407873 c.330G>T synonymous_variant 0.32 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.54 streptomycin Not assoc w R