TB-Profiler result

Run: ERR9806920
Summary

Run ID: ERR9806920

Sample name:

Date: 18-05-2023 18:43:18

Number of reads: 3130354

Percentage reads mapped: 99.75

Strain: lineage4.3.2.1

Drug-resistance: Sensitive

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 1.0
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
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
gyrB 5437 c.199delG frameshift_variant 0.14
gyrB 5520 p.Pro94Leu missense_variant 1.0
gyrB 5627 p.Ala130Thr missense_variant 0.18
gyrB 6474 p.Ser412Cys missense_variant 0.17
gyrB 7115 c.1877delT frameshift_variant 0.33
gyrB 7201 p.Glu654Asp missense_variant 0.14
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7509 p.His70Asn missense_variant 0.14
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760482 p.Gln226* stop_gained 0.14
rpoB 762387 p.Glu861* stop_gained 0.15
rpoB 762409 p.Ala868Asp missense_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765743 p.His792Tyr missense_variant 0.12
rpoC 767281 c.3912C>T synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776951 c.1530G>T synonymous_variant 0.13
mmpL5 778032 p.Gln150Arg missense_variant 0.17
mmpS5 778703 p.Asn68Ser missense_variant 0.11
mmpS5 778778 c.127delG frameshift_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781780 p.Leu74Pro missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
inhA 1674608 p.Pro136Leu missense_variant 0.12
rpsA 1834868 p.Arg443Cys missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155240 p.Ala291Val missense_variant 0.14
katG 2155703 p.Asp137Tyr missense_variant 0.17
PPE35 2167984 p.Gly877Cys missense_variant 0.14
PPE35 2169430 p.Gly395Ser missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518471 c.357C>G synonymous_variant 0.13
ahpC 2726549 c.357C>T synonymous_variant 0.11
ahpC 2726767 c.577delG frameshift_variant 0.33
Rv2752c 3065283 c.909C>A synonymous_variant 0.14
Rv2752c 3067131 c.-940G>T upstream_gene_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474976 p.Tyr324His missense_variant 0.12
fbiA 3640353 c.-190G>A upstream_gene_variant 0.19
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039871 c.834C>T synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245389 c.2157C>T synonymous_variant 0.13
embA 4245712 p.Ala827Val missense_variant 0.12
embA 4246180 p.Thr983Asn missense_variant 0.12
ubiA 4269621 c.212delT frameshift_variant 0.11
ethA 4326044 p.Gly477Asp missense_variant 0.18
ethR 4328026 p.Gly160Ser missense_variant 0.14
ethA 4328428 c.-955G>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0