TB-Profiler result

Run: SRR25827584

Summary

Run ID: SRR25827584

Sample name:

Date: 2024-04-14T15:57:25.474251

Number of reads: 7002180

Percentage reads mapped: 99.14

Median coverage: 243.0

Strain: lineage4.4.1.2;lineage4.8

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
lineage4.4.1.2 Euro-American None 0.49
lineage4.4.1 Euro-American (S-type) None 0.51
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.48
lineage4.4 Euro-American None 0.52
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.-11C>A Uncertain significance Mutation from literature
embB p.Met306Thr Uncertain significance Mutation from literature
pyrazinamide pncA p.Trp68Gly Assoc w R
streptomycin
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)
p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Ala 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 7582 p.Asp94Ala missense_variant 0.49 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
gyrA 7582 p.Asp94Gly missense_variant 0.51 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289040 p.Trp68Gly missense_variant 0.47 pyrazinamide Assoc w R
embA 4243222 c.-11C>A upstream_gene_variant 0.49 ethambutol Uncertain significance Mutation from literature
embB 4247430 p.Met306Thr missense_variant 0.45 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.51 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.44 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.44 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.55 rifampicin Not assoc w R
rpoB 760719 p.Val305Ile missense_variant 0.58 rifampicin Uncertain significance
rpoC 764840 p.Ile491Val missense_variant 0.46 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.42 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.54 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102990 p.Val18Ala missense_variant 0.44 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
PPE35 2167770 p.Ser948Ile missense_variant 0.51 pyrazinamide Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.49 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.5 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
pepQ 2860213 p.Pro69Leu missense_variant 0.45 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.53 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.44 cycloserine
Rv3083 3448460 c.-43delA upstream_gene_variant 0.18 ethionamide Uncertain significance
Rv3083 3448608 c.105G>A synonymous_variant 0.99 ethionamide Not assoc w R - Interim
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.5 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.41 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640527 c.-16G>A upstream_gene_variant 0.51 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
clpC1 4039729 p.Asp326Asn missense_variant 0.5 pyrazinamide Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.51 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.16 ethambutol
embB 4249012 c.2499G>A synonymous_variant 0.52 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 0.47 capreomycin
amikacin
kanamycin
gid 4408006 p.Val66Gly missense_variant 0.57 streptomycin