TB-Profiler result

Run: SRR23861715

Summary

Run ID: SRR23861715

Sample name:

Date: 12-04-2023 00:46:16

Number of reads: 4820077

Percentage reads mapped: 99.5

Strain: lineage4.2.1

Drug-resistance: HR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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 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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 7308 p.Asp3His missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576440 p.Cys365Gly missense_variant 0.2
mshA 576453 p.Val369Gly missense_variant 0.28
mshA 576456 p.Val370Gly missense_variant 0.27
mshA 576626 p.Thr427Pro missense_variant 0.19
mmpL5 775639 p.Ile948Val missense_variant 1.0
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 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339726 c.609A>C synonymous_variant 0.13
fbiD 3339736 p.Thr207Pro missense_variant 0.31
fbiD 3339744 c.627A>C synonymous_variant 0.17
fbiD 3339746 p.Ala210Gly missense_variant 0.47
Rv3083 3448456 c.-48G>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.19
whiB7 3568428 c.252A>G synonymous_variant 0.25
whiB7 3568441 p.Lys80Thr missense_variant 0.14
rpoA 3878597 c.-90G>C upstream_gene_variant 0.18
rpoA 3878601 c.-94C>G upstream_gene_variant 0.22
rpoA 3878609 c.-102T>G upstream_gene_variant 0.29
rpoA 3878614 c.-107A>C upstream_gene_variant 0.29
clpC1 4038932 c.1773G>A synonymous_variant 1.0
embC 4240427 p.Ser189Cys missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247007 p.Lys165Thr missense_variant 0.14
embB 4247015 p.Ser168Ala missense_variant 0.15
embB 4247028 p.Leu172Arg missense_variant 0.22
embB 4249594 c.3081G>A synonymous_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0