TB-Profiler result

Run: ERR9786508
Summary

Run ID: ERR9786508

Sample name:

Date: 2024-10-03T15:59:33.529060

Number of reads: 4215198

Percentage reads mapped: 91.53

Median coverage: 181.0

Strain: lineage4.3.3;lineage4.3.4.1

Spoligotype:

Drug-resistance: Sensitive

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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 0.99
lineage4.3.4.1 Euro-American (LAM) RD174 0.85
lineage4 Euro-American None 1.0
lineage4.3.3 Euro-American (LAM) RD115 0.18
lineage4.3.4 Euro-American (LAM) RD174 0.83
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
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 8334 p.Met345Val missense_variant 0.81 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13483 p.Ala26Thr missense_variant 0.87 isoniazid Uncertain significance
rpoB 761153 c.1347G>C synonymous_variant 0.15 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761189 c.1383T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761207 c.1401C>T synonymous_variant 0.15 rifampicin
rpoB 761213 c.1407G>C synonymous_variant 0.15 rifampicin
rpoB 761354 c.1548C>T synonymous_variant 0.14 rifampicin
rpoC 764764 c.1395T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765937 c.2568T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765967 c.2598C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766861 c.3492G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.16 rifampicin
rpoC 766876 c.3507C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766882 c.3513C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766900 c.3531T>C synonymous_variant 0.16 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.17 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.17 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767009 p.Ser1214Thr missense_variant 0.14 rifampicin
rpoC 767033 p.Ser1222Thr missense_variant 0.14 rifampicin
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
sigE 1364434 p.Arg8Trp missense_variant 0.84 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833841 c.300C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.15 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.13 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834102 c.561T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834105 c.564C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834108 c.567C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834123 c.582C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834513 c.972C>G synonymous_variant 0.15 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834555 c.1014T>G synonymous_variant 0.16 pyrazinamide
rpsA 1834606 c.1065C>G synonymous_variant 0.16 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.17 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834654 p.Glu371Asp missense_variant 0.16 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.15 pyrazinamide
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 2222854 p.Ile104Thr missense_variant 0.81 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
kasA 2518624 c.510C>G synonymous_variant 0.16 isoniazid
kasA 2518639 c.525G>C synonymous_variant 0.18 isoniazid
kasA 2518657 c.543G>C synonymous_variant 0.18 isoniazid
kasA 2518672 c.558G>C synonymous_variant 0.16 isoniazid
kasA 2518678 c.564C>T synonymous_variant 0.16 isoniazid
kasA 2518684 c.570C>G synonymous_variant 0.17 isoniazid
kasA 2518696 c.582C>G synonymous_variant 0.17 isoniazid
kasA 2518702 c.588C>T synonymous_variant 0.17 isoniazid
kasA 2518705 c.591T>C synonymous_variant 0.16 isoniazid
kasA 2518711 c.597A>G synonymous_variant 0.17 isoniazid
kasA 2518714 c.600A>C synonymous_variant 0.17 isoniazid
kasA 2518732 c.618C>G synonymous_variant 0.15 isoniazid
kasA 2518738 c.624G>C synonymous_variant 0.16 isoniazid
kasA 2518744 c.630C>T synonymous_variant 0.15 isoniazid
kasA 2518747 c.633C>G synonymous_variant 0.14 isoniazid
kasA 2518768 c.654C>T synonymous_variant 0.14 isoniazid
kasA 2518777 c.663C>T synonymous_variant 0.14 isoniazid
kasA 2518919 p.Gly269Ser missense_variant 0.15 isoniazid
Rv2477c 2783674 c.369T>C synonymous_variant 0.14 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783683 c.360A>G synonymous_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783700 p.Thr115Ser missense_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783718 c.325T>C synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783719 c.324A>G synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783751 p.Ile98Val missense_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783758 p.Asp95Glu missense_variant 0.15 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783761 c.282G>C synonymous_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783766 p.Met93Leu missense_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783776 c.267G>C synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783779 c.264T>C synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2681 2997212 c.474A>G synonymous_variant 0.16 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.95 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.8 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625711 c.903C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3625714 c.-804C>T upstream_gene_variant 0.14 rifampicin
bedaquiline
lpqB 3625735 c.-825C>T upstream_gene_variant 0.13 rifampicin
bedaquiline
rpoA 3878217 c.291A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878226 c.282C>G synonymous_variant 0.16 rifampicin
rpoA 3878232 c.276G>C synonymous_variant 0.18 rifampicin
rpoA 3878247 c.261G>C synonymous_variant 0.17 rifampicin
rpoA 3878250 c.258C>G synonymous_variant 0.17 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878284 p.Glu75Ala missense_variant 0.21 rifampicin
rpoA 3878292 c.216T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3878298 c.210A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878304 c.204G>C synonymous_variant 0.18 rifampicin
rpoA 3878310 c.198G>C synonymous_variant 0.19 rifampicin
rpoA 3878313 c.195G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878322 c.186A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878331 c.177A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878334 c.174T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878337 c.171T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 0.19 rifampicin
rpoA 3878364 c.144A>C synonymous_variant 0.18 rifampicin
rpoA 3878367 c.141C>G synonymous_variant 0.18 rifampicin
rpoA 3878376 c.132G>C synonymous_variant 0.18 rifampicin
rpoA 3878385 c.123C>G synonymous_variant 0.16 rifampicin
rpoA 3878388 c.120C>G synonymous_variant 0.16 rifampicin
rpoA 3878391 c.117T>C synonymous_variant 0.16 rifampicin
rpoA 3878415 c.93C>T synonymous_variant 0.15 rifampicin
rpoA 3878424 c.84G>C synonymous_variant 0.17 rifampicin
rpoA 3878436 c.72A>G synonymous_variant 0.17 rifampicin
rpoA 3878442 c.66G>C synonymous_variant 0.15 rifampicin
rpoA 3878742 c.-235G>A upstream_gene_variant 0.13 rifampicin
rpoA 3878749 c.-242G>T upstream_gene_variant 0.16 rifampicin
rpoA 3878761 c.-254G>C upstream_gene_variant 0.15 rifampicin
rpoA 3878764 c.-257A>G upstream_gene_variant 0.15 rifampicin
rpoA 3878785 c.-278T>G upstream_gene_variant 0.17 rifampicin
rpoA 3878788 c.-281G>C upstream_gene_variant 0.19 rifampicin Uncertain significance
rpoA 3878806 c.-299C>G upstream_gene_variant 0.18 rifampicin
rpoA 3878809 c.-302T>C upstream_gene_variant 0.18 rifampicin
rpoA 3878818 c.-311G>A upstream_gene_variant 0.17 rifampicin
rpoA 3878824 c.-317G>C upstream_gene_variant 0.17 rifampicin
rpoA 3878833 c.-326C>G upstream_gene_variant 0.16 rifampicin
rpoA 3878836 c.-331_-329delAAGinsTCC upstream_gene_variant 0.16 rifampicin
rpoA 3878853 c.-346G>A upstream_gene_variant 0.18 rifampicin
rpoA 3878878 c.-371T>C upstream_gene_variant 0.19 rifampicin Uncertain significance
rpoA 3878890 c.-383C>G upstream_gene_variant 0.21 rifampicin
rpoA 3878896 c.-389G>C upstream_gene_variant 0.19 rifampicin
rpoA 3878909 c.-402A>G upstream_gene_variant 0.21 rifampicin
rpoA 3878914 c.-407T>C upstream_gene_variant 0.21 rifampicin Uncertain significance
rpoA 3878917 c.-410G>A upstream_gene_variant 0.2 rifampicin Uncertain significance
rpoA 3878932 c.-425G>A upstream_gene_variant 0.19 rifampicin
rpoA 3878938 c.-431T>C upstream_gene_variant 0.19 rifampicin
rpoA 3878947 c.-440G>C upstream_gene_variant 0.18 rifampicin Uncertain significance
rpoA 3878968 c.-461T>C upstream_gene_variant 0.16 rifampicin Uncertain significance
rpoA 3878976 c.-469A>G upstream_gene_variant 0.15 rifampicin Uncertain significance
rpoA 3878986 c.-479G>C upstream_gene_variant 0.15 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
clpC1 4038287 c.2418C>T synonymous_variant 0.96 pyrazinamide Not assoc w R
clpC1 4039991 c.714G>A synonymous_variant 0.81 pyrazinamide Not assoc w R
embC 4241567 p.Ile569Val missense_variant 0.15 ethambutol
embC 4241572 c.1710C>G synonymous_variant 0.15 ethambutol
embC 4241578 c.1716G>C synonymous_variant 0.15 ethambutol
embC 4241584 c.1722T>C synonymous_variant 0.15 ethambutol
embC 4241587 c.1725C>G synonymous_variant 0.15 ethambutol
embC 4241591 p.Leu577Val missense_variant 0.15 ethambutol
embC 4241611 c.1749G>C synonymous_variant 0.16 ethambutol
embC 4241614 c.1752A>C synonymous_variant 0.17 ethambutol
embC 4241626 c.1764T>C synonymous_variant 0.16 ethambutol
embC 4241635 c.1773G>C synonymous_variant 0.15 ethambutol
embC 4241644 c.1782G>C synonymous_variant 0.14 ethambutol
embC 4241648 c.1786_1788delTTGinsCTC synonymous_variant 0.14 ethambutol
embC 4242182 p.Ala774Ser missense_variant 0.15 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247893 c.1380C>T synonymous_variant 0.13 ethambutol
embB 4247914 c.1401G>C synonymous_variant 0.15 ethambutol Not assoc w R - Interim
embB 4247932 c.1419C>G synonymous_variant 0.14 ethambutol
embB 4248626 p.Ala705Pro missense_variant 0.21 ethambutol
whiB6 4338555 c.-34G>A upstream_gene_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin 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 1.0 kanamycin
capreomycin
amikacin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R