TB-Profiler result

Run: ERR6358721
Summary

Run ID: ERR6358721

Sample name:

Date: 02-04-2023 02:10:11

Number of reads: 1859732

Percentage reads mapped: 99.68

Strain: lineage4.6.5;lineage4.6.1.2

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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.5 Euro-American T;LAM None 0.57
lineage4.6.1 Euro-American (Uganda) T2 RD724 0.33
lineage4.6.1.2 Euro-American T2 RD724 0.33
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 0.26 rifampicin
tlyA 1918647 p.Asn236Lys missense_variant 0.68 capreomycin
katG 2155168 p.Ser315Thr missense_variant 0.29 isoniazid
pncA 2289214 p.Gln10* stop_gained 0.37 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.39 ethambutol
ethA 4326249 c.1215_1224delGTTGAATTAC frameshift_variant 0.35 ethionamide, 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 5489 p.Ile84Val missense_variant 0.79
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 0.38
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490756 c.-27T>G upstream_gene_variant 0.58
fgd1 491134 p.Tyr118His missense_variant 0.68
mshA 576108 p.Ala254Gly missense_variant 0.16
rpoB 761406 p.Val534Met missense_variant 0.18
rpoC 764703 p.Lys445Arg missense_variant 0.17
rpoC 764810 p.Pro481Thr missense_variant 0.43
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777974 c.507C>T synonymous_variant 0.6
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 0.42
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170692 c.-80T>G upstream_gene_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714308 p.Pro342Leu missense_variant 0.42
folC 2746995 p.Val202Ile missense_variant 0.56
Rv2752c 3065920 p.Pro91Leu missense_variant 0.27
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640346 c.-196delA upstream_gene_variant 0.74
clpC1 4038332 c.2373C>T synonymous_variant 0.74
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 0.33
embB 4247024 p.Pro171Ala missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408094 p.Gly37Arg missense_variant 0.32