TB-Profiler result

Run: SRR23310811
Summary

Run ID: SRR23310811

Sample name:

Date: 13-03-2023 23:00:13

Number of reads: 1642373

Percentage reads mapped: 99.51

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 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.99
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
rpoC 765609 p.Asp747Ala missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Ala missense_variant 0.98 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 9304 p.Gly668Asp missense_variant 1.0
mshA 576616 c.1269G>C synonymous_variant 0.29
rpoC 764367 p.Gly333Ala missense_variant 0.22
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
fabG1 1673553 p.Asp38Glu missense_variant 0.21
rpsA 1833461 c.-81T>C upstream_gene_variant 0.96
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.96
PPE35 2170065 p.Ala183Gly missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289050 c.187_188insACT conservative_inframe_insertion 0.93
pepQ 2860159 p.Ala87Gly missense_variant 0.21
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.78
fbiD 3339746 p.Ala210Gly missense_variant 0.4
fprA 3473996 c.-10_-9insA upstream_gene_variant 1.0
fprA 3475324 p.Pro440Ala missense_variant 0.98
whiB7 3568428 c.252A>G synonymous_variant 0.35
rpoA 3878597 c.-90G>C upstream_gene_variant 0.22
rpoA 3878637 c.-130G>C upstream_gene_variant 0.43
rpoA 3878641 c.-134C>G upstream_gene_variant 0.4
clpC1 4040901 c.-197C>T upstream_gene_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249007 p.Pro832Ser missense_variant 1.0
embB 4249594 c.3081G>A synonymous_variant 1.0
ethA 4326569 p.Phe302Cys missense_variant 0.98
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408150 c.51delC frameshift_variant 0.97