TB-Profiler result

Run: ERR3287355

Summary

Run ID: ERR3287355

Sample name:

Date: 20-10-2023 05:45:28

Number of reads: 3729291

Percentage reads mapped: 99.69

Strain: lineage4.7;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 0.75
lineage4 Euro-American LAM;T;S;X;H None 0.28
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.73
lineage4.7 Euro-American (mainly T) T1;T5 None 0.26
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.72
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 0.75
gyrA 9304 p.Gly668Asp missense_variant 0.76
fgd1 491742 c.960T>C synonymous_variant 0.78
mshA 575907 p.Ala187Val missense_variant 0.68
ccsA 619822 c.-69G>T upstream_gene_variant 0.38
ccsA 620625 p.Ile245Met missense_variant 0.77
rpoC 763031 c.-339T>C upstream_gene_variant 0.77
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.75
mmpL5 776182 p.Asp767Asn missense_variant 0.76
mmpS5 779615 c.-710C>G upstream_gene_variant 0.72
mmpS5 779630 c.-725T>C upstream_gene_variant 0.72
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.76
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.28
rrl 1475721 n.2064C>T non_coding_transcript_exon_variant 0.3
rpsA 1834177 c.636A>C synonymous_variant 0.85
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.71
PPE35 2167926 p.Leu896Ser missense_variant 0.71
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3067039 c.-848T>C upstream_gene_variant 0.64
ald 3086788 c.-32T>C upstream_gene_variant 0.84
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.75
Rv3236c 3612813 p.Thr102Ala missense_variant 0.75
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.71
embB 4249732 c.3219C>G synonymous_variant 0.34
aftB 4267647 p.Asp397Gly missense_variant 0.58
whiB6 4338591 c.-70G>C upstream_gene_variant 0.29
whiB6 4338592 c.-71G>T upstream_gene_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.72
gid 4407927 p.Glu92Asp missense_variant 0.73