TB-Profiler result

Run: SRR1173415
Summary

Run ID: SRR1173415

Sample name:

Date: 2024-04-16T10:34:59.268938

Number of reads: 2054790

Percentage reads mapped: 88.17

Median coverage: 44.0

Strain: lineage2.2.1.1;lineage4.6.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.3
lineage2 East-Asian RD105 0.73
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.68
lineage2.2 East-Asian (Beijing) RD105;RD207 0.68
lineage4 Euro-American None 0.29
lineage4.6.1 Euro-American (Uganda) RD724 0.31
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.7
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
embB p.Glu405Asp Uncertain significance Mutation from literature
pyrazinamide pncA p.Val139Ala Assoc w R
p.Gly108Glu Assoc w R - Interim
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.517C>T 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.6 streptomycin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.34 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288826 p.Val139Ala missense_variant 0.71 pyrazinamide Assoc w R
pncA 2288919 p.Gly108Glu missense_variant 0.29 pyrazinamide Assoc w R - Interim
embA 4243217 c.-16C>T upstream_gene_variant 0.26 ethambutol Uncertain significance Mutation from literature
embB 4247728 p.Glu405Asp missense_variant 0.38 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
gyrB 5081 c.-159_-158insA upstream_gene_variant 0.26 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7539 p.Thr80Ala missense_variant 0.32 levofloxacin Not assoc w R
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 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
fgd1 491742 c.960T>C synonymous_variant 0.7 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.78 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.81 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.66 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.78 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.6 rifampicin Not assoc w R
rpoC 766699 p.Gln1110His missense_variant 0.3 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 0.67 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.66 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.58 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.64 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 0.76 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rpsA 1834177 c.636A>C synonymous_variant 0.83 pyrazinamide Not assoc w R - Interim
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 1918198 p.Leu87Val missense_variant 0.39 capreomycin
katG 2154724 p.Arg463Leu missense_variant 0.84 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.58 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
eis 2714846 p.Val163Ile missense_variant 0.6 amikacin Not assoc w R
kanamycin Not assoc w R
folC 2747195 p.Asp135Gly missense_variant 0.66 para-aminosalicylic_acid
Rv2477c 2784442 c.-400G>A upstream_gene_variant 0.62 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2681 2996876 c.138A>C synonymous_variant 0.28 capreomycin Not assoc w R
Rv2752c 3064985 p.Leu403Met missense_variant 0.24 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
ald 3086750 c.-70A>C upstream_gene_variant 0.27 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.7 cycloserine
whiB7 3568874 c.-195C>T upstream_gene_variant 0.54 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB7 3569029 c.-350A>G upstream_gene_variant 0.35 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Not assoc w R
Rv3236c 3612813 p.Thr102Ala missense_variant 0.81 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.64 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.85 bedaquiline Uncertain significance
rifampicin Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 0.53 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4139670 p.Cys29Tyr missense_variant 0.29 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Not assoc w R
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243190 c.-43G>C upstream_gene_variant 0.76 ethambutol Uncertain significance
embA 4243216 c.-17G>A upstream_gene_variant 0.74 ethambutol Uncertain significance
embA 4243460 c.228C>T synonymous_variant 0.78 ethambutol Not assoc w R
embA 4243557 p.Ala109Thr missense_variant 0.21 ethambutol Uncertain significance
embB 4247873 p.Ala454Thr missense_variant 0.7 ethambutol Uncertain significance
embB 4248115 c.1602C>T synonymous_variant 0.8 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.72 ethambutol 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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.67 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.72 streptomycin Not assoc w R