TB-Profiler result

Run: ERR6197023
Summary

Run ID: ERR6197023

Sample name:

Date: 2024-10-05T00:40:26.956228

Number of reads: 2545384

Percentage reads mapped: 95.54

Median coverage: 79.0

Strain: lineage4.3.4.2;lineage4.7

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.13
lineage4.7 Euro-American (mainly T) None 0.82
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.11
lineage4.3.4.2 Euro-American (LAM) RD174 0.15
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
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1484G>T Assoc w R
capreomycin rrs n.1484G>T Assoc w R
kanamycin rrs n.1484G>T Assoc w R
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 0.22 rifampicin Assoc w R
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.69 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.19 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
Rv0010c 13636 c.-78A>G upstream_gene_variant 0.83 isoniazid Uncertain significance
rpoC 762989 c.-381G>C upstream_gene_variant 0.15 rifampicin
rpoB 763005 p.Cys1067Val missense_variant 0.14 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 763053 c.3247T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 763578 p.Phe70Tyr missense_variant 0.12 rifampicin
rpoC 763666 c.297G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764918 p.Val517Leu missense_variant 0.14 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.16 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
Rv1129c 1253651 p.Ala295Val missense_variant 0.9 levofloxacin
moxifloxacin
isoniazid
rifampicin
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.9 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.75 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473305 n.1460G>T non_coding_transcript_exon_variant 0.72 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.74 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.9 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.9 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476262 n.2605G>A non_coding_transcript_exon_variant 0.8 capreomycin
linezolid
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476298 n.2641C>A non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476307 n.2650A>T non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476309 n.2652G>T non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1833469 c.-73G>T upstream_gene_variant 0.29 pyrazinamide Uncertain significance
rpsA 1834306 c.765T>C synonymous_variant 0.11 pyrazinamide
rpsA 1834327 c.786G>T synonymous_variant 0.12 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 0.29 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289200 c.42C>T synonymous_variant 0.89 pyrazinamide
thyA 3073868 p.Thr202Ala missense_variant 0.17 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.16 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 0.25 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840719 c.702A>G synonymous_variant 0.19 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.18 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.74 ethambutol Not assoc w R
gid 4407970 p.Pro78Leu missense_variant 0.14 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.17 streptomycin Not assoc w R