TB-Profiler result

Run: SRR1172858
Summary

Run ID: SRR1172858

Sample name:

Date: 03-04-2023 03:11:59

Number of reads: 909404

Percentage reads mapped: 96.14

Strain: lineage4.3.3

Drug-resistance: MDR-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 0.99
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.99
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472753 n.908A>G non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 1.0 ethionamide
pncA 2288565 c.377_*115del frameshift_variant&stop_lost&splice_region_variant 1.0 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 8040 p.Gly247Ser missense_variant 1.0
gyrA 8121 c.820T>C synonymous_variant 0.11
gyrA 8129 c.828T>C synonymous_variant 0.11
gyrA 8135 c.834C>G synonymous_variant 0.12
gyrA 8177 c.876A>C synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491144 p.Ala121Asp missense_variant 0.12
fgd1 491151 c.369G>A synonymous_variant 0.12
fgd1 491173 c.391C>A synonymous_variant 0.14
fgd1 491181 c.399T>C synonymous_variant 0.14
fgd1 491184 c.402A>G synonymous_variant 0.14
fgd1 491191 p.Gly137Arg missense_variant 0.14
fgd1 491194 c.412_414delCTAinsTTG synonymous_variant 0.14
fgd1 491202 c.420G>C synonymous_variant 0.14
fgd1 491203 p.Gln141Glu missense_variant 0.14
fgd1 491212 p.Ser144Arg missense_variant 0.14
fgd1 491217 c.435T>C synonymous_variant 0.14
rpoB 761547 p.Val581Met missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765937 c.2568T>C synonymous_variant 0.15
rpoC 765947 c.2578T>C synonymous_variant 0.11
rpoC 765982 c.2613C>G synonymous_variant 0.11
rpoC 765994 c.2625A>T synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781628 c.69T>C synonymous_variant 0.11
rpsL 781631 c.72G>C synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471932 n.87A>G non_coding_transcript_exon_variant 0.11
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.1
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
inhA 1673685 c.-517C>T upstream_gene_variant 0.1
fabG1 1673710 p.Leu91Ile missense_variant 0.12
fabG1 1673716 p.Ala93Lys missense_variant 0.11
fabG1 1673733 p.Met98Ile missense_variant 0.12
inhA 1673748 c.-454A>G upstream_gene_variant 0.12
fabG1 1673749 p.Lys104Arg missense_variant 0.11
fabG1 1673758 p.Lys107Glu missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877679 p.Ala277Ser missense_variant 0.11
rpoA 3877686 c.822A>G synonymous_variant 0.12
rpoA 3877692 c.816G>C synonymous_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242115 c.2253G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4407912 c.160_290del frameshift_variant 1.0