TB-Profiler result

Run: SRR6896230
Summary

Run ID: SRR6896230

Sample name:

Date: 04-04-2023 17:59:32

Number of reads: 193073

Percentage reads mapped: 99.81

Strain: lineage4.3.2.1

Drug-resistance: Sensitive

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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
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 8015 p.Gln238His missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 619831 c.-60T>G upstream_gene_variant 0.4
rpoC 764721 p.Leu451Arg missense_variant 0.2
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765523 c.2154C>T synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779578 c.-673A>G upstream_gene_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303259 p.Val110Ala missense_variant 0.22
Rv1258c 1406292 p.Gly350Val missense_variant 0.22
Rv1258c 1406513 c.828G>A synonymous_variant 0.2
Rv1258c 1406717 c.624G>A synonymous_variant 0.4
Rv1258c 1407517 c.-177G>A upstream_gene_variant 0.18
embR 1416856 c.492G>A synonymous_variant 0.5
embR 1416967 c.381C>T synonymous_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1475173 n.1516A>G non_coding_transcript_exon_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154356 p.Val586Met missense_variant 0.13
PPE35 2168470 p.Thr715Ala missense_variant 0.17
Rv1979c 2221988 p.Leu393Ile missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726265 p.Lys25Gln missense_variant 0.22
ahpC 2726506 p.Thr105Lys missense_variant 0.2
folC 2747676 c.-78C>A upstream_gene_variant 0.15
Rv2752c 3065458 c.733dupG frameshift_variant 0.29
thyX 3067755 p.Ile64Thr missense_variant 0.22
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074189 p.Gly95Ser missense_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449734 p.Arg411Trp missense_variant 0.12
fprA 3473941 c.-66A>G upstream_gene_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840232 p.Arg397Gly missense_variant 0.2
rpoA 3878111 p.Lys133Glu missense_variant 0.14
ddn 3986695 c.-149G>T upstream_gene_variant 0.18
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038717 p.Ile663Thr missense_variant 0.22
clpC1 4039215 p.Phe497Ser missense_variant 0.13
embC 4239679 c.-184T>C upstream_gene_variant 0.12
embC 4240962 c.1104delG frameshift_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246028 c.-486G>T upstream_gene_variant 0.5
aftB 4267615 p.Val408Leu missense_variant 0.13
ethA 4326851 p.Ser208Leu missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407913 p.Arg97His missense_variant 0.11
gid 4408156 p.Leu16Arg missense_variant 1.0