TB-Profiler result

Run: ERR3335755

Summary

Run ID: ERR3335755

Sample name:

Date: 21-10-2023 15:05:56

Number of reads: 6785742

Percentage reads mapped: 99.22

Strain: lineage3.1.3

Drug-resistance: Pre-XDR-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 c.1292_1294dupGCC (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Gly406Ser (1.00)
Pyrazinamide
Streptomycin R rpsL p.Lys88Met (1.00)
Fluoroquinolones R gyrB p.Thr500Asn (0.99)
Moxifloxacin R gyrB p.Thr500Asn (0.99)
Ofloxacin R gyrB p.Thr500Asn (0.99)
Levofloxacin R gyrB p.Thr500Asn (0.99)
Ciprofloxacin R gyrB p.Thr500Asn (0.99)
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
lineage3.1.3 East-African-Indian CAS 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
gyrB 6738 p.Thr500Asn missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761097 c.1292_1294dupGCC disruptive_inframe_insertion 1.0 rifampicin
rpsL 781822 p.Lys88Met missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247729 p.Gly406Ser missense_variant 1.0 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 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
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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
rpsA 1834159 c.618G>A synonymous_variant 0.99
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
Rv1979c 2222732 c.432delT frameshift_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 0.99
folC 2746876 c.723C>T synonymous_variant 0.98
Rv2752c 3065860 p.Leu111Arg missense_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841207 p.His72Tyr missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249195 c.2682C>A synonymous_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408175 p.Ala10Pro missense_variant 0.99