TB-Profiler result

Run: ERR11465015
Summary

Run ID: ERR11465015

Sample name:

Date: 2024-04-15T10:57:41.493241

Number of reads: 4549700

Percentage reads mapped: 99.59

Median coverage: 106.0

Strain: lineage4.3.4.2.1

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 1.0
lineage4 Euro-American None 1.0
lineage4.3.4.2.1 Euro-American (LAM) RD174 1.0
lineage4.3.4 Euro-American (LAM) RD174 1.0
lineage4.3.4.2 Euro-American (LAM) RD174 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
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 741 c.741T>C synonymous_variant 0.13 isoniazid Not assoc w R - Interim
dnaA 750 c.750C>G synonymous_variant 0.12 isoniazid
dnaA 756 c.756T>C synonymous_variant 0.11 isoniazid
gyrB 5611 c.372C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6140 p.Val301Leu missense_variant 0.9 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6170 p.His311Ala missense_variant 0.16 levofloxacin
moxifloxacin
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 7763 c.462T>G synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8324 c.1023T>C synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8339 c.1038A>C synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 8915 c.1614A>G synonymous_variant 0.11 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9242 c.1941A>C synonymous_variant 0.11 levofloxacin
moxifloxacin
gyrA 9248 c.1947G>C synonymous_variant 0.11 levofloxacin
moxifloxacin
gyrA 9252 p.Val651Ile missense_variant 0.12 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9267 p.Asn656Gly missense_variant 0.17 levofloxacin
moxifloxacin
gyrA 9296 c.1995T>C synonymous_variant 0.2 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Glu missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9308 c.2007C>T synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9323 c.2022C>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9335 c.2034G>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 9345 c.2044A>C synonymous_variant 0.14 levofloxacin
moxifloxacin
hadA 731789 c.-141A>G upstream_gene_variant 0.15 isoniazid
hadA 731792 c.-138G>A upstream_gene_variant 0.15 isoniazid
rpoC 764548 c.1179G>C synonymous_variant 0.15 rifampicin
rpoC 764560 c.1191T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.96 rifampicin Not assoc w R
rpoC 765611 p.His748Ser missense_variant 0.14 rifampicin Uncertain significance
rpoC 765937 c.2568T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 765979 c.2610C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766492 c.3123T>C synonymous_variant 0.13 rifampicin
rpoC 766517 p.Thr1050Ala missense_variant 0.16 rifampicin
rpoC 766522 c.3153C>A synonymous_variant 0.16 rifampicin
rpoC 766528 c.3159T>G synonymous_variant 0.14 rifampicin
rpoC 766530 p.Arg1054Gln missense_variant 0.14 rifampicin
mmpL5 775639 p.Ile948Val 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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473290 n.1445delCinsTT non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475482 n.1825A>G non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833770 p.Asn77His missense_variant 0.12 pyrazinamide
rpsA 1833781 c.240T>G synonymous_variant 0.12 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.18 pyrazinamide
rpsA 1834456 c.915T>G synonymous_variant 0.17 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.18 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.21 pyrazinamide
rpsA 1834527 p.Arg329Gln missense_variant 0.14 pyrazinamide
rpsA 1834573 c.1032G>C synonymous_variant 0.16 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 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2752c 3065947 p.Gly82Ala missense_variant 0.12 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065957 c.235T>C synonymous_variant 0.14 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065990 p.Glu68Gln missense_variant 0.12 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065994 c.198T>C synonymous_variant 0.12 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3066000 p.Met64Ile missense_variant 0.12 ethambutol Uncertain significance
moxifloxacin
levofloxacin
rifampicin Uncertain significance
isoniazid Uncertain significance
thyA 3073868 p.Thr202Ala missense_variant 1.0 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640390 c.-153A>G upstream_gene_variant 0.62 clofazimine
pretomanid
delamanid
alr 3840719 c.702A>G synonymous_variant 1.0 cycloserine
rpoA 3877695 c.813C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877794 c.714G>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoA 3877905 c.603A>C synonymous_variant 0.11 rifampicin
rpoA 3877908 c.600T>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
glpK 4138598 c.1158G>A synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138601 c.1155G>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138631 c.1125C>G synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138634 c.1122G>T synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138643 c.1113A>G synonymous_variant 0.17 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4138661 c.1095T>C synonymous_variant 0.2 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138676 c.1080T>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol 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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R