TB-Profiler result

Run: SRR6398034
Summary

Run ID: SRR6398034

Sample name:

Date: 19-10-2023 11:35:41

Number of reads: 5409714

Percentage reads mapped: 99.67

Strain: lineage4.4.1.2;lineage2.2.1

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 fabG1 c.-15C>T (0.11)
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.11)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.11
lineage4 Euro-American LAM;T;S;X;H None 0.89
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.13
lineage4.4 Euro-American S;T None 0.87
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.1
lineage4.4.1 Euro-American (S-type) S;T None 0.88
lineage4.4.1.2 Euro-American T1 None 0.88
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
fabG1 1673425 c.-15C>T upstream_gene_variant 0.11 isoniazid, ethionamide
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
fgd1 491742 c.960T>C synonymous_variant 0.13
rpoB 760947 p.Asn381His missense_variant 0.87
rpoC 763031 c.-339T>C upstream_gene_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.12
mmpS5 779565 c.-660G>C upstream_gene_variant 0.9
mmpS5 779615 c.-710C>G upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.89
katG 2154724 p.Arg463Leu missense_variant 0.16
PPE35 2167770 p.Ser948Ile missense_variant 0.85
PPE35 2167926 p.Leu896Ser missense_variant 0.12
PPE35 2169840 p.Gly258Asp missense_variant 0.9
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518699 c.585C>T synonymous_variant 0.92
pepQ 2860213 p.Pro69Leu missense_variant 0.86
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.8
Rv3083 3449347 p.Asp282Tyr missense_variant 0.84
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249012 c.2499G>A synonymous_variant 0.88
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.12
gid 4407927 p.Glu92Asp missense_variant 0.12