TB-Profiler result

Run: SRR23862142
Summary

Run ID: SRR23862142

Sample name:

Date: 12-04-2023 20:39:15

Number of reads: 4845704

Percentage reads mapped: 99.56

Strain: lineage4.1.2.1

Drug-resistance: Sensitive

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
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 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576453 p.Val369Gly missense_variant 0.27
mshA 576456 p.Val370Gly missense_variant 0.19
mshA 576489 p.Val381Gly missense_variant 0.21
mshA 576613 c.1266A>C synonymous_variant 0.19
mshA 576626 p.Thr427Pro missense_variant 0.22
rpoB 760115 c.309C>T synonymous_variant 0.99
rpoC 765150 p.Gly594Glu missense_variant 1.0
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339720 c.603C>G synonymous_variant 0.18
fbiD 3339744 c.627A>T synonymous_variant 0.29
fbiD 3339746 p.Ala210Gly missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.17
rpoA 3878591 c.-84C>G upstream_gene_variant 0.18
rpoA 3878597 c.-90G>C upstream_gene_variant 0.36
rpoA 3878600 c.-93G>C upstream_gene_variant 0.18
rpoA 3878608 c.-101C>G upstream_gene_variant 0.3
rpoA 3878609 c.-102T>G upstream_gene_variant 0.22
rpoA 3878613 c.-106A>C upstream_gene_variant 0.18
rpoA 3878638 c.-131C>G upstream_gene_variant 0.15
rpoA 3878648 c.-141C>G upstream_gene_variant 0.16
rpoA 3878653 c.-146A>C upstream_gene_variant 0.15
embC 4240427 p.Ser189Cys missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4247007 p.Lys165Thr missense_variant 0.23
embB 4247015 p.Ser168Ala missense_variant 0.33
ethR 4328045 p.Leu166Gln missense_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0