TB-Profiler result

Run: SRR7592355
Summary

Run ID: SRR7592355

Sample name:

Date: 04-04-2023 19:49:30

Number of reads: 1617238

Percentage reads mapped: 96.21

Strain: lineage4.1.4

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
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
lineage4.1.4 Euro-American T;X;H None 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 7566 p.Asp89Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
pncA 2288954 p.Lys96Asn missense_variant 1.0 pyrazinamide
ahpC 2726112 c.-81C>T upstream_gene_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4247574 p.Asp354Ala missense_variant 1.0 ethambutol
ethA 4326419 c.1054dupG frameshift_variant 1.0 ethionamide
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 5077 c.-163_-162insC upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7643 c.342C>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.29
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765651 p.Gln761Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777719 c.762G>A synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155426 p.Tyr229Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714948 p.Phe129Leu missense_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.23
Rv2752c 3065269 p.Gln308Pro missense_variant 1.0
thyX 3067947 c.-2C>T upstream_gene_variant 1.0
thyA 3074455 c.16dupG frameshift_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087538 p.Leu240Arg missense_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 1.0
fbiD 3339746 p.Ala210Gly missense_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.78
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243222 c.-11C>T upstream_gene_variant 1.0
embA 4243251 p.Glu7Lys missense_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.67
embB 4246555 c.42G>C synonymous_variant 0.73
embB 4246556 p.Ala15Pro missense_variant 0.73
embB 4246563 p.Leu17Trp missense_variant 0.6
embB 4246567 c.54G>T synonymous_variant 1.0
embB 4247016 p.Ser168Trp missense_variant 0.19
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408061 p.His48Tyr missense_variant 0.98