TB-Profiler result

Run: SRR7755679
Summary

Run ID: SRR7755679

Sample name:

Date: 2024-10-04T21:07:03.208103

Number of reads: 4835215

Percentage reads mapped: 99.58

Median coverage: 92.0

Strain: lineage4.2.1;lineage4.8

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 0.3
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.67
lineage4.2.1 Euro-American (TUR) None 0.3
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
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
katG 2155168 p.Ser315Thr missense_variant 0.29 isoniazid Assoc w R High-level resistance
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 0.24 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.24 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.73 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.57 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.26 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.84 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.25 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 0.27 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
streptomycin Not assoc w R - Interim
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.15 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
katG 2156835 c.-724C>A upstream_gene_variant 0.24 isoniazid
PPE35 2168149 p.Pro822Ser missense_variant 0.67 pyrazinamide Not assoc w R
PPE35 2168247 p.Leu789Arg missense_variant 0.68 pyrazinamide Uncertain significance
PPE35 2169879 p.Phe245Cys missense_variant 0.29 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289952 c.-711C>G upstream_gene_variant 0.91 pyrazinamide
folC 2747536 c.63G>A synonymous_variant 0.17 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.76 capreomycin
ald 3086742 c.-78A>C upstream_gene_variant 0.25 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.38 cycloserine
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.76 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.33 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878783 c.-276C>T upstream_gene_variant 0.7 rifampicin Uncertain significance
clpC1 4039729 p.Asp326Asn missense_variant 0.65 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249594 c.3081G>A synonymous_variant 0.31 ethambutol Not assoc w R - Interim
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.43 kanamycin
capreomycin
amikacin