TB-Profiler result

Run: SRR25827517
Summary

Run ID: SRR25827517

Sample name:

Date: 2024-04-15T23:26:24.521555

Number of reads: 38890734

Percentage reads mapped: 99.46

Median coverage: 822.5

Strain: lineage3.1.2;lineage4.2.2.2;lineage4.3.3

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2.2 Euro-American (Ural) None 0.27
lineage3 East-African-Indian RD750 0.18
lineage4.3 Euro-American (LAM) None 0.53
lineage3.1.2 East-African-Indian RD750 0.19
lineage4.2 Euro-American None 0.28
lineage4 Euro-American None 0.8
lineage4.3.3 Euro-American (LAM) RD115 0.53
lineage4.2.2.2 Euro-American (Ural) None 0.28
lineage3.1 East-African-Indian RD750 0.23
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.Ser493Leu Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Trp68Arg Assoc w R
c.-10T>C Uncertain significance Mutation from literature
streptomycin gid c.115delC Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Gly Assoc w R
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
gyrA 7570 p.Ala90Val missense_variant 0.53 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Gly missense_variant 0.18 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.21 rifampicin Assoc w R
rpoB 761284 p.Ser493Leu missense_variant 0.54 rifampicin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.78 isoniazid Assoc w R High-level resistance
pncA 2289040 p.Trp68Arg missense_variant 0.19 pyrazinamide Assoc w R
pncA 2289251 c.-10T>C upstream_gene_variant 0.52 pyrazinamide Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.58 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.21 ethambutol Assoc w R
gid 4408087 c.115delC frameshift_variant 0.23 streptomycin 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
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 0.54 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8688 p.Ala463Ser missense_variant 0.31 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 0.17 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 576077 c.730C>T synonymous_variant 0.27 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
Rv0565c 657425 p.Gly16Ser missense_variant 0.24 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.17 rifampicin Not assoc w R
rpoB 760321 p.Gln172Arg missense_variant 0.6 rifampicin Uncertain significance
rpoB 761032 p.Gln409Arg missense_variant 0.5 rifampicin Uncertain significance
rpoB 761489 c.1683G>A synonymous_variant 0.26 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.2 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.22 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.51 rifampicin Not assoc w R
rpoC 765463 p.Asn698Lys missense_variant 0.23 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 0.2 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 800204 c.-605T>C upstream_gene_variant 0.32 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.22 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254587 c.-53G>A upstream_gene_variant 0.27 moxifloxacin
levofloxacin
rifampicin
isoniazid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1673406 c.-796C>T upstream_gene_variant 0.57 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1834334 p.Val265Phe missense_variant 0.15 pyrazinamide
rpsA 1834836 p.Met432Thr missense_variant 0.48 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 1918104 c.165G>A synonymous_variant 0.2 capreomycin Not assoc w R - Interim
bacA 2063685 c.1044G>A synonymous_variant 0.3 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2101764 p.Gly427Ser missense_variant 0.27 ethionamide Uncertain significance
delamanid
isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.19 isoniazid Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.59 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.22 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.17 pyrazinamide Not assoc w R
PPE35 2170048 p.Leu189Val missense_variant 0.18 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.17 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.19 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.24 pyrazinamide
kasA 2518919 p.Gly269Ser missense_variant 0.56 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.14 isoniazid Not assoc w R
folC 2746340 p.Ala420Val missense_variant 0.41 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.18 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2752c 3066280 c.-89C>T upstream_gene_variant 0.25 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyA 3073868 p.Thr202Ala missense_variant 0.57 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 0.26 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.53 pyrazinamide Not assoc w R
clpC1 4040323 p.Gly128Ser missense_variant 0.18 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.2 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.19 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.16 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.31 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.26 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.22 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.22 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.25 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.23 ethambutol Not assoc w R - Interim
embB 4247028 p.Leu172Arg missense_variant 0.16 ethambutol
ethA 4327073 p.Leu134Arg missense_variant 0.21 ethionamide Uncertain significance
whiB6 4338595 c.-75delG 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 0.22 streptomycin Not assoc w R
gid 4408085 p.Glu40Gln missense_variant 0.5 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.54 streptomycin Not assoc w R