TB-Profiler result

Run: ERR4796584
Summary

Run ID: ERR4796584

Sample name:

Date: 2024-03-26T16:00:57.135037

Number of reads: 2525885

Percentage reads mapped: 93.44

Median coverage: 70.0

Strain: lineage1.2.2.2

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 1.0
lineage1.2.2.2 Indo-Oceanic RD239 1.0
lineage1 Indo-Oceanic RD239 0.98
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
dnaA 1353 c.1353T>C synonymous_variant 0.13 isoniazid
dnaA 1375 c.1375T>C synonymous_variant 0.16 isoniazid
dnaA 1383 c.1383A>G synonymous_variant 0.15 isoniazid
dnaA 1389 c.1389C>G synonymous_variant 0.15 isoniazid
dnaA 1392 c.1392A>G synonymous_variant 0.15 isoniazid
dnaA 1395 c.1395G>C synonymous_variant 0.14 isoniazid
dnaA 1404 c.1404T>C synonymous_variant 0.15 isoniazid
dnaA 1407 c.1407T>C synonymous_variant 0.13 isoniazid
dnaA 1413 c.1413A>C synonymous_variant 0.14 isoniazid
dnaA 1416 c.1416C>G synonymous_variant 0.14 isoniazid
dnaA 1428 c.1428C>G synonymous_variant 0.12 isoniazid
dnaA 1431 c.1431A>G synonymous_variant 0.13 isoniazid
dnaA 1449 c.1449G>A synonymous_variant 0.12 isoniazid
gyrB 5075 c.-165C>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 1.0 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 7943 p.Glu214Asp missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8452 p.Ala384Val missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 1.0 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 1.0 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
Rv0010c 13548 p.Thr4Ile missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 1.0 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.98 rifampicin Not assoc w R
rpoC 762989 c.-381G>C upstream_gene_variant 0.15 rifampicin
rpoC 763013 c.-357C>G upstream_gene_variant 0.2 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.77 rifampicin Not assoc w R
rpoB 763031 c.3225T>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763034 c.3228C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763884 p.Ala172Val missense_variant 0.93 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.92 rifampicin Not assoc w R
rpoC 766726 c.3357T>C synonymous_variant 0.15 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.16 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.14 rifampicin
rpoC 766801 c.3432C>G synonymous_variant 0.13 rifampicin
rpoC 767059 c.3690T>G 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
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 1.0 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254747 c.-213C>A upstream_gene_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1303884 c.954T>G synonymous_variant 0.12 clofazimine
pretomanid
delamanid
embR 1417019 p.Cys110Tyr missense_variant 1.0 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1473945 n.288T>A non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1473946 n.289A>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rpsA 1834633 c.1092A>G synonymous_variant 0.17 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834654 p.Glu371Asp missense_variant 0.13 pyrazinamide
rpsA 1834684 c.1143C>T synonymous_variant 0.14 pyrazinamide
tsnR 1853974 c.369C>T synonymous_variant 1.0 linezolid Not assoc w R
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 2062922 p.Ile603Val missense_variant 1.0 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223553 c.-389C>A upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 1.0 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 1.0 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
rpoA 3878817 c.-310T>A upstream_gene_variant 0.81 rifampicin Not assoc w R
rpoA 3878878 c.-371T>C upstream_gene_variant 0.14 rifampicin Uncertain significance
rpoA 3878890 c.-383C>G upstream_gene_variant 0.2 rifampicin
rpoA 3878909 c.-402A>G upstream_gene_variant 0.16 rifampicin
rpoA 3878914 c.-407T>C upstream_gene_variant 0.16 rifampicin Uncertain significance
clpC1 4038425 c.2280C>T synonymous_variant 0.97 pyrazinamide Not assoc w R - Interim
clpC1 4040517 p.Val63Ala missense_variant 0.92 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.98 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 1.0 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin 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 4338603 c.-82C>T 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 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 1.0 streptomycin Not assoc w R