TB-Profiler result

Run: ERR4799837

Summary

Run ID: ERR4799837

Sample name:

Date: 20-10-2023 03:31:04

Number of reads: 5060285

Percentage reads mapped: 99.55

Strain: lineage3

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
Rifampicin R rpoB p.Ser450Leu (1.00)
Isoniazid R katG p.Ser315Thr (0.97)
Ethambutol R embB p.Gly406Asp (0.99)
Pyrazinamide R pncA p.Leu172Arg (0.93)
Streptomycin R rpsL p.Lys88Arg (0.97)
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 0.97
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
rpsL 781822 p.Lys88Arg missense_variant 0.97 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
pncA 2288727 p.Leu172Arg missense_variant 0.93 pyrazinamide
embB 4247730 p.Gly406Asp missense_variant 0.99 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 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 0.99
mshA 576750 c.1407_1421dupCCGCCACTGGACGCC disruptive_inframe_insertion 0.98
rpoB 759746 c.-61C>T upstream_gene_variant 0.94
rpoC 762434 c.-936T>G upstream_gene_variant 0.96
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764840 p.Ile491Val missense_variant 0.95
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475380 n.1723C>T non_coding_transcript_exon_variant 1.0
rpsA 1833585 p.Asp15Ala missense_variant 0.93
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.97
pncA 2289365 c.-125delC upstream_gene_variant 0.95
ahpC 2726105 c.-88G>A upstream_gene_variant 0.97
pepQ 2860566 c.-148C>T upstream_gene_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 0.93
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244164 p.Leu311His missense_variant 0.95
ethR 4326874 c.-675C>T upstream_gene_variant 0.98
whiB6 4338523 c.-2T>C upstream_gene_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0