TB-Profiler result

Run: ERR108127
Summary

Run ID: ERR108127

Sample name:

Date: 20-10-2023 21:52:09

Number of reads: 8028692

Percentage reads mapped: 99.73

Strain: lineage4.3.3;lineage2.2.1.1

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 0.2
lineage4 Euro-American LAM;T;S;X;H None 0.81
lineage4.3 Euro-American (LAM) mainly-LAM None 0.82
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.18
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.17
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.83
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.16
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 8040 p.Gly247Ser missense_variant 0.82
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.2
mshA 575907 p.Ala187Val missense_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 0.19
rpoC 763031 c.-339T>C upstream_gene_variant 0.19
rpoC 764995 c.1626C>G synonymous_variant 0.83
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.18
mmpL5 776182 p.Asp767Asn missense_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 0.21
mmpS5 779675 c.-770G>A upstream_gene_variant 0.82
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
fbiC 1302818 c.-113G>C upstream_gene_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673277 c.-163_-162insT upstream_gene_variant 0.82
rpsA 1834177 c.636A>C synonymous_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 0.18
Rv1979c 2223014 p.Tyr51Asn missense_variant 0.21
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.82
eis 2714846 p.Val163Ile missense_variant 0.17
eis 2715432 c.-100C>T upstream_gene_variant 0.85
ribD 2987533 p.Gly232Ala missense_variant 0.85
thyA 3073868 p.Thr202Ala missense_variant 0.75
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449301 c.798G>A synonymous_variant 0.76
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.16
clpC1 4038287 c.2418C>T synonymous_variant 0.77
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.17
embB 4247209 c.696A>G synonymous_variant 0.86
embB 4248115 c.1602C>T synonymous_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.17
gid 4407927 p.Glu92Asp missense_variant 0.16
gid 4408156 p.Leu16Arg missense_variant 0.88