TB-Profiler result

Run: SRR29017444
Summary

Run ID: SRR29017444

Sample name:

Date: 2025-02-11T11:44:19.482456

Number of reads: 1790995

Percentage reads mapped: 99.55

Median coverage: 55.0

Strain: lineage1.1.3.3;lineage4

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.3 Indo-Oceanic RD239 0.23
lineage1.1.3.3 Indo-Oceanic RD239 0.22
lineage1.1 Indo-Oceanic RD239 0.21
lineage4 Euro-American None 0.7
lineage1 Indo-Oceanic RD239 0.2
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Arg Assoc w R
p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Leu19Arg Uncertain significance Mutation from literature
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
rpoB 761140 p.His445Arg missense_variant 0.61 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.3 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.7 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289186 p.Leu19Arg missense_variant 0.71 pyrazinamide Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.26 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 6061 p.Ser274Arg missense_variant 0.63 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.36 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 9143 c.1842T>C synonymous_variant 0.23 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 0.3 isoniazid Not assoc w R
Rv0010c 13641 c.-83A>G upstream_gene_variant 0.69 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.32 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.19 ethionamide
hadA 732127 p.Lys66Asn missense_variant 0.69 isoniazid Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.26 rifampicin Not assoc w R
nusG 734407 p.Val52Leu missense_variant 0.29 rifampicin
rpoB 759628 c.-179C>T upstream_gene_variant 0.8 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.28 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.18 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.18 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.19 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 0.25 rifampicin Not assoc w R
rpoC 767123 p.Val1252Leu missense_variant 0.32 rifampicin Uncertain significance
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 0.32 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 0.37 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.26 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1407255 p.Ala29Glu missense_variant 0.7 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1416468 p.Asp294Asn missense_variant 0.3 ethambutol Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.22 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.24 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.22 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473293 n.1448G>C non_coding_transcript_exon_variant 0.53 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrl 1475049 n.1392C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673393 c.-809G>A upstream_gene_variant 0.76 isoniazid Uncertain significance
ethionamide Uncertain significance
rpsA 1833525 c.-17C>A upstream_gene_variant 0.19 pyrazinamide
rpsA 1833584 p.Asp15Asn missense_variant 0.26 pyrazinamide
rpsA 1833614 p.Ala25Thr missense_variant 0.3 pyrazinamide Uncertain significance
tsnR 1853974 c.369C>T synonymous_variant 0.23 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.23 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 0.28 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.31 isoniazid Not assoc w R
katG 2156146 c.-35A>G upstream_gene_variant 0.24 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.34 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.27 pyrazinamide Uncertain significance
PPE35 2169779 c.834A>C synonymous_variant 0.75 pyrazinamide Not assoc w R - Interim
Rv1979c 2222308 p.Asp286Gly missense_variant 0.36 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
Rv1979c 2223712 c.-548G>A upstream_gene_variant 0.27 bedaquiline
clofazimine
pncA 2288772 p.Val157Gly missense_variant 0.33 pyrazinamide Uncertain significance
pncA 2289256 c.-15A>C upstream_gene_variant 0.63 pyrazinamide Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.15 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.26 isoniazid
folC 2746365 c.1234C>T synonymous_variant 0.23 para-aminosalicylic_acid
Rv2681 2997944 c.1206C>T synonymous_variant 0.32 capreomycin Not assoc w R - Interim
Rv2752c 3064632 c.1560C>T synonymous_variant 0.34 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
ald 3086788 c.-32T>C upstream_gene_variant 0.31 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.31 ethionamide Uncertain significance
lpqB 3623435 c.1476G>A synonymous_variant 0.35 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3624486 p.Asp142Gly missense_variant 0.3 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.32 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.23 pyrazinamide Not assoc w R - Interim
panD 4043957 p.Asp109Asn missense_variant 0.73 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.21 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 4238922 c.-941G>A upstream_gene_variant 0.37 ethambutol Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.3 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.18 ethambutol Not assoc w R
embC 4241736 p.Val625Ala missense_variant 0.22 ethambutol Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.24 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.25 ethambutol Not assoc w R
embB 4247351 p.Asp280Tyr missense_variant 0.25 ethambutol Uncertain significance
embB 4247646 p.Glu378Ala missense_variant 0.31 ethambutol Not assoc w R
aftB 4267431 p.Ser469Leu missense_variant 0.14 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.36 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.23 ethambutol Not assoc w R
ethA 4328317 c.-844C>T upstream_gene_variant 0.69 ethionamide
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 0.31 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 0.24 streptomycin Not assoc w R
gid 4407780 c.423G>A synonymous_variant 0.2 streptomycin Not assoc w R - Interim
gid 4407873 c.330G>T synonymous_variant 0.27 streptomycin Not assoc w R
gid 4407980 p.Pro75Ser missense_variant 0.17 streptomycin Uncertain significance