TB-Profiler result

Run: SRR833050
Summary

Run ID: SRR833050

Sample name:

Date: 04-04-2023 20:59:12

Number of reads: 310934

Percentage reads mapped: 85.39

Strain: lineage4

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
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 761110 p.Asp435Gly missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673432 c.-8T>A upstream_gene_variant 0.83 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288785 c.456dupC frameshift_variant 1.0 pyrazinamide, pyrazinamide
ethA 4327484 c.-11A>G upstream_gene_variant 0.9 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9697 p.Lys799Thr missense_variant 0.18
mshA 575988 p.Ile214Ser missense_variant 0.4
rpoB 761299 p.Ala498Val missense_variant 0.67
rpoB 761353 p.Gly516Ala missense_variant 0.4
rpoB 761404 p.His533Arg missense_variant 0.5
rpoB 763123 p.Ile1106Thr missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775618 p.Pro955Ser missense_variant 0.5
mmpL5 776027 c.2454G>T synonymous_variant 0.25
mmpL5 776925 p.Thr519Met missense_variant 0.13
mmpR5 779487 c.498A>C stop_lost&splice_region_variant 0.29
mmpS5 779511 c.-606T>C upstream_gene_variant 0.33
mmpS5 779561 c.-662_-657delGGGCAA upstream_gene_variant 0.33
mmpS5 779574 c.-669T>A upstream_gene_variant 0.33
mmpS5 779578 c.-673A>T upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302778 c.-153G>T upstream_gene_variant 0.18
fbiC 1302800 c.-130_-121delGGTGCCGGAC upstream_gene_variant 0.33
fbiC 1302818 c.-113G>A upstream_gene_variant 0.33
fbiC 1303181 p.Ile84Ser missense_variant 0.25
fbiC 1304605 p.Tyr559His missense_variant 0.25
fbiC 1305057 p.Met709Ile missense_variant 0.25
embR 1416245 p.His368Arg missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101904 p.Ala380Asp missense_variant 0.2
PPE35 2168402 c.2211A>C synonymous_variant 0.22
PPE35 2168679 c.1933delA frameshift_variant 0.33
Rv1979c 2223051 p.Glu38Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289658 c.-417C>T upstream_gene_variant 0.2
eis 2715405 c.-73T>C upstream_gene_variant 0.22
pepQ 2859793 p.Asp209Ala missense_variant 0.67
pepQ 2860022 p.Glu133* stop_gained 0.4
pepQ 2860289 c.130C>T synonymous_variant 0.25
pepQ 2860446 c.-28T>G upstream_gene_variant 0.25
ribD 2986990 p.Gly51Ala missense_variant 0.67
Rv2752c 3064646 p.Glu516* stop_gained 0.4
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
fbiB 3640629 c.-906T>C upstream_gene_variant 0.67
fbiB 3641073 c.-462T>G upstream_gene_variant 0.5
alr 3840664 p.Pro253Thr missense_variant 0.4
ddn 3987183 c.345_348dupCGAC frameshift_variant 0.29
clpC1 4039249 p.Glu486Lys missense_variant 0.25
clpC1 4039254 p.Ile484Thr missense_variant 0.29
clpC1 4040373 p.Gly111Val missense_variant 0.43
embC 4239967 c.105G>A synonymous_variant 1.0
embC 4240028 p.Thr56Ala missense_variant 1.0
embC 4242069 p.Val736Gly missense_variant 0.33
embC 4242072 c.2212dupC frameshift_variant 0.4
embA 4246141 p.Leu970Trp missense_variant 0.67
ubiA 4269271 p.Val188Ala missense_variant 1.0
ethR 4326703 c.-846T>C upstream_gene_variant 0.17
ethA 4326964 p.Asp170Glu missense_variant 0.33
ethR 4328129 p.Val194Ala missense_variant 0.4
whiB6 4338595 c.-75delG upstream_gene_variant 1.0