TB-Profiler result

Run: SRR7341648
Summary

Run ID: SRR7341648

Sample name:

Date: 19-10-2023 19:08:28

Number of reads: 4057738

Percentage reads mapped: 99.55

Strain: lineage4.1.2.1

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Gln432Pro (1.00)
Isoniazid R katG c.1548_1549dupGG (0.99), katG c.2_6dupTGCCC (1.00), ahpC c.-52C>T (1.00)
Ethambutol R embA c.-12C>T (1.00)
Pyrazinamide R pncA p.Gln10Arg (1.00)
Streptomycin
Fluoroquinolones R gyrA p.Ser91Pro (1.00)
Moxifloxacin R gyrA p.Ser91Pro (1.00)
Ofloxacin R gyrA p.Ser91Pro (1.00)
Levofloxacin R gyrA p.Ser91Pro (1.00)
Ciprofloxacin R gyrA p.Ser91Pro (1.00)
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
gyrA 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761101 p.Gln432Pro missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2154562 c.1548_1549dupGG frameshift_variant 0.99 isoniazid
katG 2156105 c.2_6dupTGCCC frameshift_variant 1.0 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 1.0 pyrazinamide
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575332 c.-16T>G upstream_gene_variant 0.99
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.19
mshA 576221 p.Gly292Arg missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 762112 p.Asn769Thr missense_variant 1.0
rpoB 762714 p.Val970Met missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766759 c.3390G>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474578 n.921A>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154647 p.Arg489Cys missense_variant 1.0
katG 2156309 c.-198G>C upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086728 c.-92C>T upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087307 c.489delG frameshift_variant 0.73
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
ubiA 4269671 p.Val55Leu missense_variant 1.0
ethA 4326908 p.Thr189Lys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0