TB-Profiler result

Run: SRR25827488
Summary

Run ID: SRR25827488

Sample name:

Date: 2024-03-25T20:11:06.718082

Number of reads: 10347093

Percentage reads mapped: 98.8

Median coverage: 351.0

Strain: lineage1.2.2.2;lineage4.3.3

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 0.34
lineage1.2.2 Indo-Oceanic RD239 0.5
lineage1.2.2.2 Indo-Oceanic RD239 0.52
lineage4 Euro-American None 0.35
lineage1 Indo-Oceanic RD239 0.5
lineage4.3.3 Euro-American (LAM) RD115 0.34
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
p.Ile491Phe Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
c.72_73dupTC Assoc w R High-level resistance
ethambutol
pyrazinamide pncA p.Phe58Cys Assoc w R - Interim
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 thyA p.Thr22Ala Mutation from literature
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 0.69 rifampicin Assoc w R
rpoB 761277 p.Ile491Phe missense_variant 0.34 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.48 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
katG 2156038 c.72_73dupTC frameshift_variant 0.25 isoniazid Assoc w R High-level resistance
pncA 2289069 p.Phe58Cys missense_variant 0.37 pyrazinamide Assoc w R - Interim
pncA 2289228 p.Ile5Ser missense_variant 0.12 pyrazinamide Assoc w R
thyA 3074408 p.Thr22Ala missense_variant 0.13 para-aminosalicylic_acid 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
gyrB 5075 c.-165C>T upstream_gene_variant 0.49 levofloxacin
moxifloxacin
gyrB 5201 c.-39A>G upstream_gene_variant 0.56 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.47 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 7158 c.1931_1933delCCG disruptive_inframe_deletion 0.51 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7268 c.-34C>T upstream_gene_variant 0.47 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 8040 p.Gly247Ser missense_variant 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8452 p.Ala384Val missense_variant 0.5 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.54 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 0.51 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.3 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.34 isoniazid Not assoc w R
Rv0010c 13636 c.-78A>G upstream_gene_variant 0.33 isoniazid Uncertain significance
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.55 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.66 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.19 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.52 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.48 rifampicin Not assoc w R
rpoB 761276 c.1470G>T synonymous_variant 0.35 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 0.62 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.47 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.47 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.37 rifampicin Not assoc w R
rpoC 765862 p.Phe831Leu missense_variant 0.32 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 0.66 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.13 clofazimine
bedaquiline
rpsL 781241 c.-319C>T upstream_gene_variant 0.45 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800233 c.-576G>A upstream_gene_variant 0.59 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.52 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.65 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406170 p.Gly391Arg missense_variant 0.49 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.16 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.48 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.51 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.53 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471754 n.-92T>G upstream_gene_variant 0.48 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
rpsA 1834836 p.Met432Thr missense_variant 0.28 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.49 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 0.58 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2101756 c.1287G>T synonymous_variant 0.61 ethionamide
delamanid
isoniazid
katG 2154724 p.Arg463Leu missense_variant 0.69 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.32 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.7 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.59 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.56 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.5 clofazimine Not assoc w R
bedaquiline Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.5 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.33 isoniazid
eis 2714177 p.Leu386Ile missense_variant 0.48 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726051 c.-142G>A upstream_gene_variant 0.52 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.42 para-aminosalicylic_acid
thyX 3067949 c.-4C>T upstream_gene_variant 0.15 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.32 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.52 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.13 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.5 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 3626467 c.147G>A synonymous_variant 0.53 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.38 pyrazinamide Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.56 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.51 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 0.51 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.47 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245835 p.Leu868Arg missense_variant 0.16 ethambutol
embA 4245969 p.Pro913Ser missense_variant 0.51 ethambutol Not assoc w R
embB 4247015 p.Ser168Ala missense_variant 0.21 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.56 ethambutol Not assoc w R
embB 4247847 p.Gln445Arg missense_variant 0.17 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.54 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.54 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.5 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.53 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.65 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338533 c.-12T>C upstream_gene_variant 0.49 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 0.48 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 0.63 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.49 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.15 streptomycin Not assoc w R
gid 4408156 p.Leu16Arg missense_variant 0.35 streptomycin Not assoc w R