TB-Profiler result

Run: SRR6797541
Summary

Run ID: SRR6797541

Sample name:

Date: 2024-04-15T22:54:47.495681

Number of reads: 2484835

Percentage reads mapped: 99.37

Median coverage: 56.0

Strain: lineage1.2.2.2;lineage4.1.1.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 0.77
lineage1.2.2.2 Indo-Oceanic RD239 0.78
lineage4.1 Euro-American None 0.18
lineage4.1.1.1 Euro-American (X-type) RD183 0.21
lineage4 Euro-American None 0.23
lineage4.1.1 Euro-American (X-type) None 0.22
lineage1 Indo-Oceanic RD239 0.74
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
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
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 0.8 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.79 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.77 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 0.88 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.85 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 0.76 isoniazid Not assoc w R
Rv0010c 13379 p.Arg60Ser missense_variant 0.26 isoniazid Uncertain significance
Rv0010c 13460 c.99T>C synonymous_variant 0.72 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.7 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.8 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.78 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
fgd1 491781 c.999G>A synonymous_variant 0.24 clofazimine
pretomanid
delamanid
Rv0565c 657269 p.Ser68Pro missense_variant 0.15 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.78 ethionamide
hadA 732367 c.438C>A synonymous_variant 0.81 isoniazid Not assoc w R - Interim
nusG 734116 c.-138T>C upstream_gene_variant 0.79 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.78 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.69 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.7 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.31 rifampicin Not assoc w R
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 0.84 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800219 c.-590T>C upstream_gene_variant 0.21 linezolid
rplC 800357 c.-452C>A upstream_gene_variant 0.65 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.83 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embR 1417019 p.Cys110Tyr missense_variant 0.71 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.82 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.86 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853629 c.24G>A synonymous_variant 0.2 linezolid Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.71 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
tlyA 1918004 p.Gln22Arg missense_variant 0.85 capreomycin
tlyA 1918162 p.Glu75Lys missense_variant 0.79 capreomycin Uncertain significance
bacA 2062922 p.Ile603Val missense_variant 0.67 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.88 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.87 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.81 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.74 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.83 clofazimine Not assoc w R
bedaquiline Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.87 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.72 isoniazid
folC 2746590 p.Gly337Cys missense_variant 0.18 para-aminosalicylic_acid
pepQ 2860186 p.Ala78Val missense_variant 0.79 clofazimine
bedaquiline
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.77 ethionamide Uncertain significance
Rv3236c 3612984 p.Asn45His missense_variant 0.69 pyrazinamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.73 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 0.66 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
fbiA 3641447 p.Thr302Met missense_variant 0.19 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
alr 3840864 p.Asp186Gly missense_variant 0.24 cycloserine
rpoA 3877553 p.Glu319Lys missense_variant 0.22 rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.81 pyrazinamide Not assoc w R - Interim
panD 4044305 c.-24C>T upstream_gene_variant 0.9 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.68 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 4240390 p.Asn176Lys missense_variant 0.25 ethambutol Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 0.61 ethambutol Not assoc w R
embC 4240897 c.1035C>G synonymous_variant 0.17 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.78 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 0.23 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.71 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.74 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.25 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.84 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.74 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.71 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.83 ethionamide Uncertain significance
ethA 4327161 p.Ile105Leu missense_variant 0.18 ethionamide Uncertain significance
ethA 4327297 p.Met59Ile missense_variant 0.85 ethionamide
ethR 4327694 p.Asp49Ala missense_variant 0.77 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.74 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
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 0.81 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 4407551 p.Met218Val missense_variant 0.15 streptomycin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 0.84 streptomycin Not assoc w R
gid 4407611 p.Pro198Ala missense_variant 0.14 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.87 streptomycin Not assoc w R