TB-Profiler result

Run: ERR11465033
Summary

Run ID: ERR11465033

Sample name:

Date: 2024-10-03T21:12:35.479370

Number of reads: 8352131

Percentage reads mapped: 99.68

Median coverage: 210.0

Strain: lineage4.4.1.1;lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.4.1 Euro-American (S-type) None 0.69
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.3
lineage4.4.1.1 Euro-American None 0.69
lineage4.4 Euro-American None 0.7
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.Met306Val Assoc w R
pyrazinamide pncA c.158delA Assoc w R
streptomycin rrs n.517C>T Assoc w R
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 0.52 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.45 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.28 isoniazid Assoc w R High-level resistance
pncA 2289083 c.158delA frameshift_variant 0.28 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.26 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.6 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9138 p.Gln613Glu missense_variant 0.62 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.68 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.17 isoniazid
ethionamide
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.3 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.31 rifampicin Not assoc w R
rpoB 762475 p.Gly890Val missense_variant 0.3 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777416 c.1065G>T synonymous_variant 0.68 bedaquiline Not assoc w R - Interim
clofazimine 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 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.46 capreomycin Not assoc w R
linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.61 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
tlyA 1918420 p.Ala161Thr missense_variant 0.65 capreomycin
ndh 2102990 p.Val18Ala missense_variant 0.77 isoniazid Not assoc w R
delamanid Uncertain significance
ethionamide Uncertain significance
PPE35 2168149 p.Pro822Ser missense_variant 0.26 pyrazinamide Not assoc w R
PPE35 2168479 p.Thr712Pro missense_variant 0.67 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.82 pyrazinamide 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
eis 2715432 c.-100C>T upstream_gene_variant 0.44 kanamycin
amikacin
folC 2746529 p.Ala357Val missense_variant 0.35 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.34 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.65 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.99 ethionamide Not assoc w R - Interim
whiB7 3568779 c.-100T>C upstream_gene_variant 0.73 kanamycin Not assoc w R
amikacin Not assoc w R
streptomycin Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.73 pyrazinamide Not assoc w R
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.25 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.79 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4039729 p.Asp326Asn missense_variant 0.26 pyrazinamide Not assoc w R
embC 4238963 c.-900C>T upstream_gene_variant 0.73 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.27 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.14 ethambutol Not assoc w R - Interim
ethA 4326153 p.Arg441Cys missense_variant 0.35 ethionamide Uncertain significance
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 0.74 kanamycin
capreomycin
amikacin