TB-Profiler result

Run: ERR9806790
Summary

Run ID: ERR9806790

Sample name:

Date: 18-05-2023 14:52:48

Number of reads: 133783

Percentage reads mapped: 98.55

Strain: lineage4.9;lineage2.2

Drug-resistance: RR-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.Ser450Phe (0.80)
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
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
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.37
lineage4.9 Euro-American (H37Rv-like) T1 None 0.88
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.Ser450Phe missense_variant 0.8 rifampicin
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
gyrB 6148 c.909C>A synonymous_variant 0.33
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8987 c.1686C>A synonymous_variant 0.67
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576434 p.Gln363Lys missense_variant 0.67
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763500 p.Asp44Ala missense_variant 0.29
rpoC 765944 p.Gly859Cys missense_variant 0.5
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800941 p.Asp45Tyr missense_variant 0.2
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834162 p.Gln207His missense_variant 0.5
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103226 c.-184C>G upstream_gene_variant 1.0
katG 2154239 p.Thr625Ala missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155560 c.552C>A synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747420 p.Pro60His missense_variant 0.4
Rv2752c 3065402 c.790C>A synonymous_variant 0.67
ald 3086739 c.-81G>A upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474827 p.Ser274Tyr missense_variant 0.4
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840912 p.Ala170Glu missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0