TB-Profiler result

Run: ERR4799668

Summary

Run ID: ERR4799668

Sample name:

Date: 20-10-2023 03:59:52

Number of reads: 2734600

Percentage reads mapped: 99.38

Strain: lineage3

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 p.Asp435Tyr (1.00)
Isoniazid R fabG1 c.-17G>T (0.96), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Leu (1.00)
Pyrazinamide R pncA p.Gln10His (0.78)
Streptomycin
Fluoroquinolones R gyrA p.Ser91Pro (0.97)
Moxifloxacin R gyrA p.Ser91Pro (0.97)
Ofloxacin R gyrA p.Ser91Pro (0.97)
Levofloxacin R gyrA p.Ser91Pro (0.97)
Ciprofloxacin R gyrA p.Ser91Pro (0.97)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-37G>T (0.77)
Cycloserine
Ethionamide R fabG1 c.-17G>T (0.96), ethA p.Pro378Leu (0.99)
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 0.98
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
gyrA 7572 p.Ser91Pro missense_variant 0.97 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
fabG1 1673423 c.-17G>T upstream_gene_variant 0.96 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289212 p.Gln10His missense_variant 0.78 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 0.77 kanamycin
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
ethA 4326341 p.Pro378Leu missense_variant 0.99 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 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.98
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417040 p.Leu103Pro missense_variant 0.96
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
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 0.94
ahpC 2726105 c.-88G>A upstream_gene_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087014 c.196_197dupGC frameshift_variant 0.29
ald 3087255 c.437dupC frameshift_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612109 p.Phe336Leu missense_variant 1.0
alr 3841429 c.-10delA upstream_gene_variant 0.54
embC 4242075 p.Arg738Gln missense_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243228 c.-5G>A upstream_gene_variant 0.97
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408060 p.His48Pro missense_variant 0.98