TB-Profiler result

Run: SRR14807625
Summary

Run ID: SRR14807625

Sample name:

Date: 2024-04-14T19:41:55.982212

Number of reads: 1929958

Percentage reads mapped: 99.65

Median coverage: 60.0

Strain: lineage4.2.1;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
lineage4.3 Euro-American (LAM) None 0.51
lineage4.2 Euro-American None 0.47
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) None 0.46
lineage4.3.3 Euro-American (LAM) RD115 0.54
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Trp Assoc w R
p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Ser297Ala Uncertain significance Mutation from literature
p.Met306Ile Assoc w R
pyrazinamide pncA p.Gln10Arg Assoc w R
c.7delG Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Ala Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Asp94Ala Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
c.-12C>T Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA c.531dupC Assoc w R
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 7582 p.Asp94Ala missense_variant 0.57 moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
levofloxacin Assoc w R
rpoB 761155 p.Ser450Trp missense_variant 0.5 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.5 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.6 streptomycin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.55 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.45 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289213 p.Gln10Arg missense_variant 0.46 pyrazinamide Assoc w R
pncA 2289234 c.7delG frameshift_variant 0.57 pyrazinamide Assoc w R
eis 2715342 c.-10G>A upstream_gene_variant 0.48 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
eis 2715344 c.-12C>T upstream_gene_variant 0.56 kanamycin Assoc w R
embB 4247402 p.Ser297Ala missense_variant 0.51 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.47 ethambutol Assoc w R
ethA 4326942 c.531dupC frameshift_variant 0.55 ethionamide 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 0.57 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 491247 c.465C>T synonymous_variant 0.49 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
ccsA 619969 p.Val27Ile missense_variant 0.58 capreomycin Not assoc w R - Interim
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 656356 c.1114dupG frameshift_variant 0.56 ethionamide Uncertain significance
Rv0565c 656832 c.639G>A synonymous_variant 0.59 ethionamide Not assoc w R - Interim
rpoB 759862 p.Gln19Arg missense_variant 0.6 rifampicin Uncertain significance
rpoC 764817 p.Val483Gly missense_variant 0.43 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.49 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 0.98 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 0.44 linezolid
fbiC 1303095 c.165G>A synonymous_variant 0.55 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834836 p.Met432Thr missense_variant 0.66 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
bacA 2063685 c.1044G>A synonymous_variant 0.53 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 0.56 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2156196 c.-85C>T upstream_gene_variant 0.51 isoniazid Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.41 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.41 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.43 para-aminosalicylic_acid
Rv2752c 3066102 p.Asn30Lys missense_variant 0.66 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 0.57 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 0.4 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3623222 c.1689A>G synonymous_variant 0.4 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.43 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.6 pyrazinamide Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.38 ethambutol Not assoc w R - Interim
ubiA 4269124 p.Ala237Val missense_variant 0.4 ethambutol Uncertain significance
ethA 4326467 p.Asp336Gly missense_variant 0.48 ethionamide
ethA 4326632 p.His281Pro missense_variant 0.46 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.37 ethionamide
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 4408156 p.Leu16Arg missense_variant 0.6 streptomycin Not assoc w R