TB-Profiler result

Run: SRR6832725
Summary

Run ID: SRR6832725

Sample name:

Date: 04-04-2023 17:36:24

Number of reads: 2836505

Percentage reads mapped: 99.46

Strain: lineage4.2.1

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
lineage4.2 Euro-American H;T;LAM None 0.94
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.94
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.Asp435Val missense_variant 0.11 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.93 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.9 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.14 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.95 ethambutol
gid 4407918 c.284delT frameshift_variant 0.91 streptomycin
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 765608 p.Asp747His missense_variant 0.92
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304962 p.Trp678Gly missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.83
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747536 c.63G>A synonymous_variant 0.87
ald 3086742 c.-78A>C upstream_gene_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249594 c.3081G>A synonymous_variant 0.93
ethA 4328376 c.-903G>C upstream_gene_variant 0.89
whiB6 4338595 c.-75delG upstream_gene_variant 1.0