TB-Profiler result

Run: ERR3509850
Summary

Run ID: ERR3509850

Sample name:

Date: 2024-04-14T16:22:37.213764

Number of reads: 2897663

Percentage reads mapped: 94.56

Median coverage: 94.0

Strain: lineage4.3.4.2.1

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 1.0
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.98
lineage4.3.4 Euro-American (LAM) RD174 1.0
lineage4.3.4.2 Euro-American (LAM) RD174 0.98
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
ahpC c.-52C>T Uncertain significance Mutation from literature
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
embB p.Met306Leu Assoc w R
pyrazinamide pncA c.419delG Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA c.32delG 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
rpoB 761155 p.Ser450Leu missense_variant 0.92 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.98 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288822 c.419delG frameshift_variant 1.0 pyrazinamide Assoc w R
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid Uncertain significance Mutation from literature
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Leu missense_variant 0.98 ethambutol Assoc w R
ethA 4327441 c.32delG frameshift_variant 1.0 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
gyrB 6140 p.Val301Leu missense_variant 0.98 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8795 c.1494C>T synonymous_variant 0.97 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 764083 c.714A>G synonymous_variant 0.13 rifampicin
rpoC 764098 c.729A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764101 c.732C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764102 p.Val245Ile missense_variant 0.14 rifampicin
rpoC 764110 c.741C>G synonymous_variant 0.14 rifampicin
rpoC 764112 p.Tyr248Phe missense_variant 0.13 rifampicin
rpoC 764116 c.747C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764131 c.762T>C synonymous_variant 0.13 rifampicin
rpoC 764140 c.771C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764188 c.819A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764257 c.888G>C synonymous_variant 0.13 rifampicin
rpoC 764353 c.984G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764365 c.996C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764703 p.Lys445Arg missense_variant 0.9 rifampicin Uncertain significance
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765625 c.2256C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 766894 c.3525T>C synonymous_variant 0.13 rifampicin
rpoC 766895 c.3526T>C synonymous_variant 0.13 rifampicin
rpoC 766972 c.3603G>C synonymous_variant 0.12 rifampicin
rpoC 766975 c.3606C>T synonymous_variant 0.12 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 779609 c.-704C>T upstream_gene_variant 1.0 clofazimine
bedaquiline
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 1475881 n.2224T>C non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289909 c.-668G>A upstream_gene_variant 1.0 pyrazinamide
thyX 3067718 c.228C>G synonymous_variant 0.13 para-aminosalicylic_acid
thyX 3067721 c.225T>C synonymous_variant 0.13 para-aminosalicylic_acid
thyX 3067742 c.204A>G synonymous_variant 0.12 para-aminosalicylic_acid
thyA 3073868 p.Thr202Ala missense_variant 0.97 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3840719 c.702A>G synonymous_variant 1.0 cycloserine
clpC1 4038287 c.2418C>T synonymous_variant 0.91 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 0.99 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 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R