TB-Profiler result

Run: ERR4812285
Summary

Run ID: ERR4812285

Sample name:

Date: 20-10-2023 04:35:07

Number of reads: 4082725

Percentage reads mapped: 99.55

Strain: lineage4.1.2.1;lineage2.2.1

Drug-resistance: Sensitive

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
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 East-Asian Beijing RD105 0.37
lineage4 Euro-American LAM;T;S;X;H None 0.65
lineage4.1 Euro-American T;X;H None 0.61
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.34
lineage4.1.2 Euro-American T;H None 0.64
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.36
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.63
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
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 491591 p.Lys270Met missense_variant 0.63
fgd1 491742 c.960T>C synonymous_variant 0.36
mshA 575679 p.Asn111Ser missense_variant 0.6
mshA 575907 p.Ala187Val missense_variant 0.57
ccsA 620625 p.Ile245Met missense_variant 0.32
rpoB 760115 c.309C>T synonymous_variant 0.58
rpoB 760555 p.Glu250Gly missense_variant 0.66
rpoC 763031 c.-339T>C upstream_gene_variant 0.39
rpoC 765150 p.Gly594Glu missense_variant 0.62
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.4
mmpL5 776182 p.Asp767Asn missense_variant 0.36
mmpS5 779615 c.-710C>G upstream_gene_variant 0.28
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302920 c.-11G>A upstream_gene_variant 0.68
Rv1258c 1406760 c.580_581insC frameshift_variant 0.31
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473614 n.-44C>T upstream_gene_variant 0.39
rpsA 1834177 c.636A>C synonymous_variant 0.38
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 0.38
Rv1979c 2221889 p.Val426Ile missense_variant 0.43
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.61
folC 2746277 p.Asp441Gly missense_variant 0.65
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087358 p.Gly180Ala missense_variant 0.6
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.42
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.62
embA 4243460 c.228C>T synonymous_variant 0.46
embA 4246085 p.Glu951Asp missense_variant 0.32
embB 4247873 p.Ala454Thr missense_variant 0.39
aftB 4267647 p.Asp397Gly missense_variant 0.35
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.4
gid 4407927 p.Glu92Asp missense_variant 0.32
gid 4408315 c.-113C>T upstream_gene_variant 0.29