TB-Profiler result

Run: ERR6197021
Summary

Run ID: ERR6197021

Sample name:

Date: 2024-10-04T14:57:50.730346

Number of reads: 2482394

Percentage reads mapped: 94.98

Median coverage: 77.0

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 0.45
lineage4.7 Euro-American (mainly T) None 0.49
lineage4 Euro-American None 1.0
lineage4.3.4 Euro-American (LAM) RD174 0.48
lineage4.3.4.2 Euro-American (LAM) RD174 0.49
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 embB p.Met306Ile Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 0.34 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.51 isoniazid Assoc w R High-level resistance
embB 4247431 p.Met306Ile missense_variant 0.59 ethambutol 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
gyrB 6140 p.Val301Leu missense_variant 0.33 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.28 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13636 c.-78A>G upstream_gene_variant 0.51 isoniazid Uncertain significance
rpoC 762989 c.-381G>C upstream_gene_variant 0.14 rifampicin
rpoB 763005 p.Cys1067Val missense_variant 0.15 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoB 763053 c.3247T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 763615 c.246G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763620 p.Arg84Gln missense_variant 0.12 rifampicin
rpoC 763622 p.Ala85Ser missense_variant 0.16 rifampicin Uncertain significance
rpoC 763630 c.261G>T synonymous_variant 0.12 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763642 c.273G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763663 c.294C>T synonymous_variant 0.13 rifampicin
rpoC 763666 c.297G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763669 c.300C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763672 c.303C>A synonymous_variant 0.14 rifampicin
rpoC 763696 c.327T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763699 c.330G>T synonymous_variant 0.14 rifampicin
rpoC 763702 c.333C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763705 c.336G>C synonymous_variant 0.12 rifampicin
rpoC 763708 c.339G>C synonymous_variant 0.13 rifampicin
rpoC 763714 c.345G>T synonymous_variant 0.12 rifampicin
rpoC 763717 c.348T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763720 c.351G>T synonymous_variant 0.12 rifampicin
rpoC 763729 c.360G>T synonymous_variant 0.12 rifampicin
rpoC 763732 c.363C>T synonymous_variant 0.14 rifampicin
rpoC 764918 p.Val517Leu missense_variant 0.5 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 0.51 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 0.57 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 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
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 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.71 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476262 n.2605G>A non_coding_transcript_exon_variant 0.73 capreomycin
linezolid
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 1.0 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 0.87 capreomycin
linezolid
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 1.0 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 0.88 capreomycin
linezolid
rrl 1476309 n.2652G>T non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
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 0.4 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 1834249 c.708T>C synonymous_variant 0.1 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
rpsA 1834306 c.765T>C synonymous_variant 0.11 pyrazinamide
rpsA 1834312 c.771G>A synonymous_variant 0.12 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 0.26 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 0.51 pyrazinamide
thyA 3073868 p.Thr202Ala missense_variant 0.54 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.51 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.48 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.41 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiA 3641119 p.Ser193Pro missense_variant 0.47 pretomanid
delamanid
clofazimine
alr 3840719 c.702A>G synonymous_variant 0.33 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.47 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 0.42 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
gid 4407970 p.Pro78Leu missense_variant 0.4 streptomycin Uncertain significance
gid 4408156 p.Leu16Arg missense_variant 0.3 streptomycin Not assoc w R