TB-Profiler result

Run: SRR1172203
Summary

Run ID: SRR1172203

Sample name:

Date: 03-04-2023 02:59:13

Number of reads: 3057876

Percentage reads mapped: 99.4

Strain: lineage4.3

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 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.95 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
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 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765569 p.Ala734Thr missense_variant 0.62
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154240 p.Met624Ile missense_variant 1.0
katG 2156138 c.-27A>G upstream_gene_variant 1.0
katG 2156549 c.-438A>C upstream_gene_variant 0.9
PPE35 2169320 p.Leu431Phe missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715555 c.-223G>A upstream_gene_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
fbiA 3640381 c.-162T>C upstream_gene_variant 0.45
clpC1 4038287 c.2418C>T synonymous_variant 0.98
embC 4240172 p.Val104Met missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4268096 c.741C>A synonymous_variant 1.0
ubiA 4269148 p.Val229Gly missense_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407807 p.Asp132Glu missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0