TB-Profiler result

Run: ERR9786554
Summary

Run ID: ERR9786554

Sample name:

Date: 2024-10-04T20:41:40.769915

Number of reads: 978187

Percentage reads mapped: 99.53

Median coverage: 40.0

Strain: lineage1.1.1;lineage4.1.1.3;lineage4.6.2.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.78
lineage4.6.2 Euro-American RD726 0.73
lineage4.1 Euro-American None 0.1
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.76
lineage1.1 Indo-Oceanic RD239 0.12
lineage4.1.1.3 Euro-American (X-type) RD193 0.09
lineage4 Euro-American None 0.94
lineage4.1.1 Euro-American (X-type) None 0.08
lineage1 Indo-Oceanic RD239 0.05
lineage1.1.1 Indo-Oceanic RD239 0.07
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
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
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 6112 p.Met291Ile missense_variant 0.12 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 8452 p.Ala384Val missense_variant 0.15 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.16 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.17 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.25 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.17 ethionamide Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.2 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 778298 c.183G>A synonymous_variant 0.65 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
embR 1417793 c.-446C>T upstream_gene_variant 0.17 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrl 1473791 n.134A>G non_coding_transcript_exon_variant 0.18 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
bacA 2063187 c.1542C>T synonymous_variant 0.82 kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2155389 c.723C>G synonymous_variant 0.77 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.27 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.26 pyrazinamide Uncertain significance
PPE35 2169829 p.Ala262Thr missense_variant 0.17 pyrazinamide Uncertain significance
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.81 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.11 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223124 p.Leu14Arg missense_variant 0.17 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2996208 p.Ala35Asp missense_variant 0.84 capreomycin Uncertain significance
thyX 3067474 p.Pro158Ala missense_variant 0.71 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.26 cycloserine
Rv3083 3448288 c.-216T>C upstream_gene_variant 0.12 ethionamide
Rv3083 3448567 p.His22Asp missense_variant 0.71 ethionamide Uncertain significance
Rv3236c 3612571 c.546C>T synonymous_variant 0.77 pyrazinamide Not assoc w R
lpqB 3623201 c.1710G>A synonymous_variant 0.17 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
lpqB 3624739 p.Ala58Ser missense_variant 0.82 rifampicin Uncertain significance
bedaquiline Uncertain significance
embC 4242550 c.2688C>G synonymous_variant 0.75 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245745 p.Pro838Leu missense_variant 0.52 ethambutol Uncertain significance
aftB 4267272 p.Lys522Arg missense_variant 0.82 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.13 ethambutol Not assoc w R
ethA 4326739 c.735C>G synonymous_variant 0.7 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 0.69 ethionamide Not assoc w R - Interim
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