TB-Profiler result

Run: ERR11465361
Summary

Run ID: ERR11465361

Sample name:

Date: 2024-10-04T17:13:41.223188

Number of reads: 1600070

Percentage reads mapped: 99.14

Median coverage: 37.0

Strain: lineage4.3.4.1

Spoligotype:

Drug-resistance: MDR-TB

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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
lineage4.3.4.1 Euro-American (LAM) RD174 1.0
lineage4 Euro-American None 1.0
lineage4.3.4 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 rpoB p.His445Ser Assoc w R
p.Ala451Val Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Arg Assoc w R
pyrazinamide
streptomycin rrs n.462C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide ethA p.Gln449* Assoc w R
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
rpoB 761139 p.His445Ser missense_variant 1.0 rifampicin Assoc w R
rpoB 761158 p.Ala451Val missense_variant 1.0 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4248003 p.Gln497Arg missense_variant 0.98 ethambutol Assoc w R
ethA 4326129 p.Gln449* stop_gained 1.0 ethionamide Assoc w R
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 1452 p.Met484Ile missense_variant 1.0 isoniazid Uncertain significance
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13483 p.Ala26Thr missense_variant 1.0 isoniazid Uncertain significance
nusG 734532 c.279A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
mmaA3 737358 c.792A>C synonymous_variant 0.13 isoniazid
rpoB 760670 c.864G>C synonymous_variant 0.14 rifampicin
rpoB 760674 c.868T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761273 c.1467T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761282 c.1476C>T synonymous_variant 0.22 rifampicin
rpoC 763666 c.297G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.91 rifampicin Not assoc w R
rpoC 766426 c.3057C>T synonymous_variant 0.19 rifampicin
rpoC 766429 c.3060C>G synonymous_variant 0.19 rifampicin
rpoC 766624 c.3255G>C synonymous_variant 0.12 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>A synonymous_variant 0.2 rifampicin
rpoC 767152 c.3783T>G synonymous_variant 0.16 rifampicin
rpoC 767155 c.3786C>G synonymous_variant 0.17 rifampicin
rpoC 767167 c.3798C>T synonymous_variant 0.2 rifampicin
rpoC 767180 p.Ala1271Pro missense_variant 0.14 rifampicin
rpoC 767191 c.3822C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
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 1.0 pyrazinamide Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472314 n.469A>G non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472315 n.470T>C non_coding_transcript_exon_variant 0.14 kanamycin
capreomycin
streptomycin
amikacin
rrl 1474716 n.1059A>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476580 n.2923G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rpsA 1833928 c.387G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833958 p.Ile139Met missense_variant 0.94 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 1.0 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
folC 2747371 c.228C>G synonymous_variant 0.21 para-aminosalicylic_acid
Rv2477c 2783620 c.423C>G synonymous_variant 0.12 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783626 p.Ala139Ser missense_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783632 c.411C>G synonymous_variant 0.12 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2752c 3064523 p.Glu557Lys missense_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
ethambutol
thyA 3073868 p.Thr202Ala missense_variant 0.97 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 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3627323 c.-712_-710delTTGinsCTC upstream_gene_variant 0.16 rifampicin
bedaquiline
fbiA 3640381 c.-162T>C upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
rpoA 3877818 c.690A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoA 3877839 c.669G>T synonymous_variant 0.27 rifampicin
rpoA 3877848 c.660C>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3877857 c.651G>A synonymous_variant 0.19 rifampicin
clpC1 4038287 c.2418C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
clpC1 4039991 c.714G>A synonymous_variant 1.0 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_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
gid 4408156 p.Leu16Arg missense_variant 1.0 streptomycin Not assoc w R