TB-Profiler result

Run: ERR12268442
Summary

Run ID: ERR12268442

Sample name:

Date: 2024-10-05T09:21:26.286981

Number of reads: 1959918

Percentage reads mapped: 97.38

Median coverage: 60.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.2 Euro-American None 1.0
lineage4.1.2.1 Euro-American (Haarlem) RD182 1.0
lineage4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin rpsL p.Lys88Gln Assoc w R - Interim
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
rpsL 781821 p.Lys88Gln missense_variant 0.91 streptomycin Assoc w R - Interim
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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8987 c.1686C>G synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8990 c.1689C>G synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8996 c.1695T>C synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9335 c.2034G>C synonymous_variant 0.12 levofloxacin
moxifloxacin
fgd1 491591 p.Lys270Met missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 1.0 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.96 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.93 rifampicin Not assoc w R
rpoB 761645 c.1839C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 1.0 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
rpsL 781865 c.306G>C synonymous_variant 0.12 streptomycin
rpsL 781868 c.309T>C synonymous_variant 0.12 streptomycin
rpsL 781877 c.318T>C synonymous_variant 0.12 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.12 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.13 streptomycin
rplC 800537 c.-272C>T upstream_gene_variant 0.16 linezolid
rplC 800540 c.-269T>C upstream_gene_variant 0.16 linezolid
rplC 800546 c.-263T>G upstream_gene_variant 0.18 linezolid
rplC 800567 c.-242A>G upstream_gene_variant 0.17 linezolid
rplC 800582 c.-227C>G upstream_gene_variant 0.16 linezolid
rplC 800612 c.-197A>G upstream_gene_variant 0.18 linezolid
rplC 800618 c.-191T>C upstream_gene_variant 0.18 linezolid
rplC 800627 c.-182C>T upstream_gene_variant 0.17 linezolid
rplC 800648 c.-161A>T upstream_gene_variant 0.2 linezolid
rplC 800654 c.-155T>C upstream_gene_variant 0.19 linezolid
rplC 800693 c.-116A>G upstream_gene_variant 0.18 linezolid
rplC 800703 c.-106T>C upstream_gene_variant 0.19 linezolid
rplC 800715 c.-94A>C upstream_gene_variant 0.19 linezolid
rplC 800720 c.-89T>C upstream_gene_variant 0.2 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.19 linezolid
rplC 800844 c.36T>C synonymous_variant 0.16 linezolid
rplC 800865 c.57A>G synonymous_variant 0.12 linezolid
rplC 800867 p.Ser20Asn missense_variant 0.12 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674537 c.336C>G synonymous_variant 0.13 isoniazid
ethionamide
inhA 1674542 p.Ala114Glu missense_variant 0.12 isoniazid
ethionamide
inhA 1674546 c.345T>C synonymous_variant 0.12 isoniazid
ethionamide
inhA 1674561 c.360C>T synonymous_variant 0.12 isoniazid
ethionamide
inhA 1674582 c.381T>C synonymous_variant 0.13 isoniazid
ethionamide
inhA 1674585 c.384T>C synonymous_variant 0.14 isoniazid
ethionamide
inhA 1674589 p.Met130Leu missense_variant 0.14 isoniazid
ethionamide
inhA 1674597 c.396G>A synonymous_variant 0.13 isoniazid
ethionamide
inhA 1674601 p.Leu134Thr missense_variant 0.13 isoniazid
ethionamide
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
bacA 2064447 c.282C>T synonymous_variant 1.0 kanamycin Not assoc w R - Interim
capreomycin
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
ribD 2986827 c.-12G>A upstream_gene_variant 1.0 para-aminosalicylic_acid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.14 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.18 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878824 c.-317G>C upstream_gene_variant 0.12 rifampicin
rpoA 3878909 c.-402A>G upstream_gene_variant 0.12 rifampicin
rpoA 3878914 c.-407T>C upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoA 3878917 c.-410G>A upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoA 3878938 c.-431T>C upstream_gene_variant 0.13 rifampicin
rpoA 3878947 c.-440G>C upstream_gene_variant 0.13 rifampicin Uncertain significance
rpoA 3878986 c.-479G>C upstream_gene_variant 0.14 rifampicin
rpoA 3878998 c.-491C>G upstream_gene_variant 0.16 rifampicin Uncertain significance
rpoA 3879005 c.-499_-498delAAinsCG upstream_gene_variant 0.15 rifampicin
rpoA 3879013 c.-506A>G upstream_gene_variant 0.16 rifampicin
rpoA 3879079 c.-572A>G upstream_gene_variant 0.14 rifampicin
rpoA 3879088 c.-581A>C upstream_gene_variant 0.14 rifampicin
rpoA 3879094 c.-587T>C upstream_gene_variant 0.15 rifampicin
rpoA 3879121 c.-614T>G upstream_gene_variant 0.15 rifampicin
rpoA 3879127 c.-620T>C upstream_gene_variant 0.15 rifampicin
clpC1 4038683 c.2022T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4038695 c.2010C>G synonymous_variant 0.13 pyrazinamide
clpC1 4038770 c.1935C>T synonymous_variant 0.12 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.12 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.13 pyrazinamide
clpC1 4038812 c.1893T>C synonymous_variant 0.14 pyrazinamide
embC 4239298 c.-565C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 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
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin