TB-Profiler result

Run: SRR1710076

Summary

Run ID: SRR1710076

Sample name:

Date: 19-10-2023 20:39:49

Number of reads: 9615946

Percentage reads mapped: 99.57

Strain: lineage2.2.2

Drug-resistance: Pre-XDR-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), rpoB p.Pro454Leu (1.00)
Isoniazid R fabG1 c.-15C>T (1.00)
Ethambutol R embB p.Met306Leu (1.00)
Pyrazinamide R pncA c.422delA (0.86), pncA c.422delA (0.86)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrA p.Ala90Val (0.79), gyrA p.Asp94Gly (0.23)
Moxifloxacin R gyrA p.Ala90Val (0.79), gyrA p.Asp94Gly (0.23)
Ofloxacin R gyrA p.Ala90Val (0.79), gyrA p.Asp94Gly (0.23)
Levofloxacin R gyrA p.Ala90Val (0.79), gyrA p.Asp94Gly (0.23)
Ciprofloxacin R gyrA p.Ala90Val (0.79), gyrA p.Asp94Gly (0.23)
Aminoglycosides R rrs n.1402C>T (0.99)
Amikacin R rrs n.1402C>T (0.99)
Capreomycin R rrs n.1402C>T (0.99)
Kanamycin R rrs n.1402C>T (0.99)
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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 1.0
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
gyrA 7570 p.Ala90Val missense_variant 0.79 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.23 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoB 761167 p.Pro454Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473247 n.1402C>T non_coding_transcript_exon_variant 0.99 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2288819 c.422delA frameshift_variant 0.86 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
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
rpoB 761583 p.His593Tyr missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155607 p.Gly169Ser missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223256 c.-92C>A upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747470 p.Ile43Ala missense_variant 1.0
Rv2752c 3065072 p.Gly374Arg missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243195 c.-37delT upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326356 p.Met373Thr missense_variant 1.0
whiB6 4338365 p.Cys53Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0