TB-Profiler result

Run: SRR4033986
Summary

Run ID: SRR4033986

Sample name:

Date: 04-04-2023 06:29:29

Number of reads: 1256115

Percentage reads mapped: 99.6

Strain: lineage4.3.2.1

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
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
katG 2155433 c.678delG frameshift_variant 0.12 isoniazid
ethA 4326652 c.821delA frameshift_variant 0.12 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 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762843 p.Phe1013Ile missense_variant 0.15
rpoB 763038 c.3235delC frameshift_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781392 c.-168C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303632 c.702T>C synonymous_variant 0.14
fbiC 1304277 c.1347G>T synonymous_variant 0.33
fbiC 1304426 p.Leu499Pro missense_variant 0.4
embR 1416916 c.430_431delGA frameshift_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471666 n.-180A>C upstream_gene_variant 0.97
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167924 p.Gly897Cys missense_variant 0.11
PPE35 2169320 p.Leu431Phe missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289853 c.-612G>T upstream_gene_variant 0.12
kasA 2518415 p.Pro101Thr missense_variant 0.17
eis 2714312 p.Thr341Ala missense_variant 0.12
ahpC 2726293 p.Tyr34Cys missense_variant 0.96
folC 2747557 c.42C>T synonymous_variant 0.11
thyA 3073806 c.666C>G synonymous_variant 0.28
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449247 c.744C>A synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474148 c.142C>T synonymous_variant 0.13
alr 3840790 p.Gln211* stop_gained 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039835 c.870C>T synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247610 p.Ser366Leu missense_variant 0.12
embB 4247892 p.Arg460His missense_variant 0.12
whiB6 4338275 c.246delC frameshift_variant 0.14
whiB6 4338297 c.225G>A synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407557 p.Ala216Thr missense_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 1.0