TB-Profiler result

Run: ERR3132130
Summary

Run ID: ERR3132130

Sample name:

Date: 01-04-2023 00:22:35

Number of reads: 2157068

Percentage reads mapped: 99.75

Strain: lineage4.6.1.2;lineage4.6.1.1

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
lineage4.6.1 Euro-American (Uganda) T2 RD724 1.0
lineage4.6.1.2 Euro-American T2 RD724 0.82
lineage4.6.1.1 Euro-American T2-Uganda RD724 0.18
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 0.8 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.85 isoniazid
pncA 2289114 p.His43Pro missense_variant 0.79 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.84 ethambutol
ethA 4326249 c.1215_1224delGTTGAATTAC frameshift_variant 0.85 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
gyrA 7054 c.-248C>T upstream_gene_variant 0.21
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7539 p.Thr80Ala missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764660 p.Val431Met missense_variant 0.8
rpoC 764810 p.Pro481Thr missense_variant 0.76
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416410 p.Leu313Arg missense_variant 0.81
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474234 n.577G>A non_coding_transcript_exon_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155413 c.699G>A synonymous_variant 0.14
PPE35 2170692 c.-80T>G upstream_gene_variant 0.84
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714308 p.Pro342Leu missense_variant 0.8
Rv2752c 3065920 p.Pro91Leu missense_variant 0.84
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245055 p.Thr608Asn missense_variant 0.74
ubiA 4269124 p.Ala237Val missense_variant 0.78
ethA 4328329 c.-856C>G upstream_gene_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408094 p.Gly37Arg missense_variant 0.85