TB-Profiler result

Run: SRR3675476
Summary

Run ID: SRR3675476

Sample name:

Date: 04-04-2023 05:29:16

Number of reads: 260444

Percentage reads mapped: 99.03

Strain: lineage4

Drug-resistance: Other

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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
tlyA 1918647 p.Asn236Lys missense_variant 1.0 capreomycin
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 5086 c.-154A>C upstream_gene_variant 0.18
gyrB 7144 p.Gln635His missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575315 c.-33G>A upstream_gene_variant 0.8
rpoB 759620 c.-187A>C upstream_gene_variant 0.38
rpoC 763178 c.-192G>A upstream_gene_variant 0.29
rpoC 764808 p.Arg480His missense_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777974 c.507C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416324 p.Asn342Tyr missense_variant 0.17
embR 1417202 p.Pro49His missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473963 n.306G>A non_coding_transcript_exon_variant 0.15
rrl 1476483 n.2826G>T non_coding_transcript_exon_variant 0.11
inhA 1674222 c.21C>T synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154254 p.Ser620Cys missense_variant 0.33
PPE35 2167814 c.2799C>T synonymous_variant 0.2
PPE35 2169125 p.Val496Ile missense_variant 0.16
PPE35 2169278 c.1335T>C synonymous_variant 0.25
PPE35 2169281 c.1332T>G synonymous_variant 0.25
PPE35 2169287 c.1326T>C synonymous_variant 0.22
PPE35 2169890 c.723C>T synonymous_variant 0.18
PPE35 2169893 c.720C>A synonymous_variant 0.18
PPE35 2169902 p.Leu237Phe missense_variant 0.21
PPE35 2169910 p.Asn235Tyr missense_variant 0.14
PPE35 2170357 p.Ala86Ser missense_variant 0.33
PPE35 2170359 p.Gln85Arg missense_variant 0.33
PPE35 2170363 p.Glu84Gln missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.29
folC 2746995 p.Val202Ile missense_variant 1.0
pepQ 2860338 c.81G>A synonymous_variant 0.25
ald 3087095 p.Phe92Leu missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878207 p.Gly101Cys missense_variant 0.25
rpoA 3878366 p.Gly48* stop_gained 0.22
clpC1 4040594 c.110delT frameshift_variant 0.22
clpC1 4040623 p.Ile28Phe missense_variant 0.25
clpC1 4040633 c.72C>T synonymous_variant 0.2
embC 4239973 c.111T>G synonymous_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326721 p.Ser251Arg missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0