TB-Profiler result

Run: ERR9806739
Summary

Run ID: ERR9806739

Sample name:

Date: 18-05-2023 14:29:42

Number of reads: 101700

Percentage reads mapped: 97.52

Strain: lineage4;lineage2.2

Drug-resistance: MDR-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.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (1.00), ahpC c.-52C>T (1.00)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00)
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 0.19
lineage4 Euro-American LAM;T;S;X;H None 0.98
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.05
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.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 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 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764861 c.1492C>T synonymous_variant 0.4
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776447 c.2034A>G synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305029 p.Val700Ala missense_variant 0.4
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrl 1474254 n.597C>T non_coding_transcript_exon_variant 0.5
rpsA 1833953 p.Leu138Val missense_variant 0.4
rpsA 1834177 c.636A>C synonymous_variant 1.0
katG 2154410 p.Thr568Pro missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
eis 2715299 p.Asp12Asn missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
whiB7 3568632 c.48G>A synonymous_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267936 p.Val301Leu missense_variant 0.67
aftB 4267974 p.Ser288* stop_gained 0.67
whiB6 4338595 c.-75delG upstream_gene_variant 1.0