TB-Profiler result

Run: ERR4828397
Summary

Run ID: ERR4828397

Sample name:

Date: 20-10-2023 13:57:23

Number of reads: 1794448

Percentage reads mapped: 99.59

Strain: lineage4.5;lineage2.2.1

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Thr (0.73)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.62)
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 East-Asian Beijing RD105 0.68
lineage4 Euro-American LAM;T;S;X;H None 0.33
lineage4.5 Euro-American H;T RD122 0.3
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.67
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.65
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
rpsL 781687 p.Lys43Arg missense_variant 0.62 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.73 isoniazid
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 0.98
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7892 c.591G>A synonymous_variant 0.32
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9524 c.2223G>A synonymous_variant 0.58
fgd1 491742 c.960T>C synonymous_variant 0.76
ccsA 620029 c.139C>T synonymous_variant 0.3
ccsA 620625 p.Ile245Met missense_variant 0.8
rpoB 759724 c.-83A>G upstream_gene_variant 0.5
rpoC 763031 c.-339T>C upstream_gene_variant 0.73
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.74
mmpS5 779615 c.-710C>G upstream_gene_variant 0.76
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.72
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.59
tlyA 1917972 c.33A>G synonymous_variant 0.98
katG 2154724 p.Arg463Leu missense_variant 0.72
PPE35 2167926 p.Leu896Ser missense_variant 0.68
PPE35 2170568 p.Ile15Met missense_variant 0.45
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.71
Rv3083 3449945 p.Gly481Asp missense_variant 0.74
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.59
clpC1 4038318 p.Pro796Leu missense_variant 0.47
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242775 c.-458G>A upstream_gene_variant 0.3
embA 4243460 c.228C>T synonymous_variant 0.67
embA 4246449 p.Val1073Ile missense_variant 0.32
aftB 4267647 p.Asp397Gly missense_variant 0.69
ethA 4326676 p.Ser266Arg missense_variant 0.75
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.65
gid 4407927 p.Glu92Asp missense_variant 0.52