TB-Profiler result

Run: SRR24114355
Summary

Run ID: SRR24114355

Sample name:

Date: 16-04-2023 21:19:08

Number of reads: 3291284

Percentage reads mapped: 99.62

Strain: lineage3.1.2.1

Drug-resistance: MDR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser428Ile (1.00)
Isoniazid R fabG1 c.-8T>G (0.72)
Ethambutol
Pyrazinamide R pncA p.Lys96Asn (1.00)
Streptomycin R gid c.102dupG (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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 1.0
lineage3.1.2.1 East-African-Indian CAS2 RD750 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 761089 p.Ser428Ile missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>G upstream_gene_variant 0.72 isoniazid
pncA 2288954 p.Lys96Asn missense_variant 1.0 pyrazinamide
gid 4408100 c.102dupG frameshift_variant 1.0 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
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.5
mshA 576613 c.1266A>C synonymous_variant 0.33
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764367 p.Gly333Ala missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.16
mmpR5 779339 p.Leu117Arg 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
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.16
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.26
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087818 p.Cys333Trp missense_variant 0.11
fbiD 3339734 p.Ala206Gly missense_variant 0.58
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.38
embC 4240409 p.Pro183Ala missense_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338420 c.83_101dupAGGTCCCGCTCGGCGTTTG frameshift_variant&stop_gained 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0