TB-Profiler result

Run: ERR4831634
Summary

Run ID: ERR4831634

Sample name:

Date: 2024-04-15T19:00:22.218901

Number of reads: 1335387

Percentage reads mapped: 99.41

Median coverage: 42.0

Strain: lineage1.1.1;lineage2.2.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.32
lineage1.1 Indo-Oceanic RD239 0.72
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.27
lineage2.2 East-Asian (Beijing) RD105;RD207 0.33
lineage1 Indo-Oceanic RD239 0.72
lineage1.1.1 Indo-Oceanic RD239 0.64
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ile317Val Uncertain significance Mutation from literature
p.Ser315Asn Assoc w R High-level resistance
ethambutol embB p.Gly406Ala Assoc w R
pyrazinamide pncA p.Ile5Ser Assoc w R
streptomycin rpsL p.Lys43Arg 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
rpsL 781687 p.Lys43Arg missense_variant 0.45 streptomycin Assoc w R
katG 2155163 p.Ile317Val missense_variant 0.37 isoniazid Uncertain significance Mutation from literature
katG 2155168 p.Ser315Asn missense_variant 0.39 isoniazid Assoc w R High-level resistance
pncA 2289228 p.Ile5Ser missense_variant 0.38 pyrazinamide Assoc w R
embB 4247730 p.Gly406Ala missense_variant 0.22 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
gyrB 5627 p.Ala130Ser missense_variant 0.8 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.76 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 8452 p.Ala384Val missense_variant 0.71 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.71 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 13275 p.Tyr95Cys missense_variant 0.75 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.76 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.62 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.59 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.26 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.53 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.34 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.32 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.63 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.79 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.71 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.74 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.81 rifampicin Not assoc w R
rpoC 766487 p.Pro1040Ala missense_variant 0.24 rifampicin Uncertain significance
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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.3 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.36 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781694 c.135G>A synonymous_variant 0.56 streptomycin Not assoc w R - Interim
rplC 800349 c.-460C>G upstream_gene_variant 0.76 linezolid Uncertain significance
rplC 800357 c.-452C>A upstream_gene_variant 0.79 linezolid Not assoc w R
Rv1129c 1254543 c.-9T>G upstream_gene_variant 0.62 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.38 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.62 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.58 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.6 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473162 n.1317C>T non_coding_transcript_exon_variant 0.88 streptomycin
kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 0.61 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.37 pyrazinamide Not assoc w R - Interim
rpsA 1834319 p.Val260Ile missense_variant 0.67 pyrazinamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.73 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.77 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 0.56 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063106 c.1623G>A synonymous_variant 0.64 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.64 pyrazinamide Uncertain significance
PPE35 2168500 p.Ser705Ala missense_variant 0.66 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.73 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223144 p.Arg7Ser missense_variant 0.82 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223758 c.-594A>G upstream_gene_variant 0.67 clofazimine
bedaquiline
kasA 2518132 c.18C>T synonymous_variant 0.55 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.86 isoniazid
ahpC 2726763 p.Leu191Phe missense_variant 0.72 isoniazid Uncertain significance
Rv2752c 3064632 c.1560C>T synonymous_variant 0.59 ethambutol Not assoc w R
moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3338931 c.-187C>A upstream_gene_variant 0.21 clofazimine
pretomanid
delamanid
Rv3083 3448714 p.Asp71His missense_variant 0.74 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.22 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.7 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.38 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840571 p.Val284Leu missense_variant 0.22 cycloserine
rpoA 3878630 c.-124delC upstream_gene_variant 0.82 rifampicin Not assoc w R
clpC1 4038545 c.2160C>T synonymous_variant 0.61 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.6 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.6 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.69 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.76 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.41 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.63 ethambutol Not assoc w R
embA 4244096 c.864C>T synonymous_variant 0.62 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.71 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.71 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.73 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.73 ethambutol Not assoc w R
whiB6 4338242 p.Gln94Glu missense_variant 0.77 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin 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 4338603 c.-82C>T upstream_gene_variant 0.85 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 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.66 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.26 streptomycin Not assoc w R