TB-Profiler result

Run: SRR1013576
Summary

Run ID: SRR1013576

Sample name:

Date: 02-04-2023 15:56:26

Number of reads: 4635387

Percentage reads mapped: 99.44

Strain: lineage4

Drug-resistance: HR-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
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
gyrB 6735 p.Asn499Thr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.74 kanamycin, capreomycin, aminoglycosides, amikacin
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2288824 c.417dupG frameshift_variant 1.0 pyrazinamide, pyrazinamide
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 1.0
gyrA 8147 p.Asn282Lys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 760090 c.289_294dupATGTCG conservative_inframe_insertion 0.85
rpoB 760101 p.Leu99Met missense_variant 0.15
rpoB 761099 c.1294_1296dupCAA conservative_inframe_insertion 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779339 p.Leu117Arg missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304501 p.Ala524Gly missense_variant 1.0
fbiC 1305357 c.2427C>G synonymous_variant 1.0
Rv1258c 1406189 c.1152A>G synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918073 p.Ala45Asp missense_variant 0.12
PPE35 2168742 p.Gly624Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
panD 4044296 c.-15A>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269148 p.Val229Gly missense_variant 1.0
ethA 4327376 p.Ala33Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0