TB-Profiler result

Run: ERR4799166
Summary

Run ID: ERR4799166

Sample name:

Date: 20-10-2023 03:13:29

Number of reads: 2902462

Percentage reads mapped: 99.65

Strain: lineage3.1.2.1

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 (0.95)
Isoniazid R katG p.Ser315Thr (0.95)
Ethambutol R embB p.Gly406Ala (0.99)
Pyrazinamide R pncA p.Asp8Glu (0.94)
Streptomycin R gid c.518dupA (0.96)
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 0.98
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.96
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 0.95
lineage3.1.2.1 East-African-Indian CAS2 RD750 0.95
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 0.95 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.95 isoniazid
pncA 2289218 p.Asp8Glu missense_variant 0.94 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.99 ethambutol
gid 4407684 c.518dupA frameshift_variant 0.96 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 0.99
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.99
rpoB 759746 c.-61C>T upstream_gene_variant 0.97
rpoC 762434 c.-936T>G upstream_gene_variant 0.98
rpoC 763031 c.-339T>C upstream_gene_variant 0.96
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
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 0.98
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 0.95
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 0.96
ahpC 2726105 c.-88G>A upstream_gene_variant 0.94
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 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245626 c.-888G>A upstream_gene_variant 0.95
ubiA 4269737 p.Leu33Val missense_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0