TB-Profiler result

Run: SRR22873602
Summary

Run ID: SRR22873602

Sample name:

Date: 10-02-2024 20:21:13

Number of reads: 19535632

Percentage reads mapped: 99.62

Strain: lineage2.2.1

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 c.1297_1299dupTTC (0.34), rpoB c.1297_1299dupTTC (0.34), rpoB p.Ser450Leu (0.62)
Isoniazid R fabG1 c.-15C>T (1.00), katG p.Tyr337Cys (0.57), katG p.Ser315Thr (0.43), ahpC c.-52C>T (0.55)
Ethambutol R embB p.Met306Val (0.61), embB p.Gly406Asp (0.39), embB p.Gln497Pro (0.35)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrB p.Ser447Phe (0.44), gyrA p.Asp94Ala (0.42), gyrA p.Asp94Gly (0.58)
Moxifloxacin R gyrB p.Ser447Phe (0.44), gyrA p.Asp94Ala (0.42), gyrA p.Asp94Gly (0.58)
Ofloxacin R gyrB p.Ser447Phe (0.44), gyrA p.Asp94Ala (0.42), gyrA p.Asp94Gly (0.58)
Levofloxacin R gyrB p.Ser447Phe (0.44), gyrA p.Asp94Ala (0.42), gyrA p.Asp94Gly (0.58)
Ciprofloxacin R gyrB p.Ser447Phe (0.44), gyrA p.Asp94Ala (0.42), gyrA p.Asp94Gly (0.58)
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), ethA c.312dupG (0.20)
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
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrB 6579 p.Ser447Phe missense_variant 0.44 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.42 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.58 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761102 c.1297_1299dupTTC conservative_inframe_insertion 0.34 rifampicin, rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.62 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155102 p.Tyr337Cys missense_variant 0.57 isoniazid
katG 2155168 p.Ser315Thr missense_variant 0.43 isoniazid
ahpC 2726141 c.-52C>T upstream_gene_variant 0.55 isoniazid
embB 4247429 p.Met306Val missense_variant 0.61 ethambutol
embB 4247730 p.Gly406Asp missense_variant 0.39 ethambutol
embB 4248003 p.Gln497Pro missense_variant 0.35 ethambutol
ethA 4327161 c.312dupG frameshift_variant 0.2 ethionamide
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 764916 p.Leu516Pro missense_variant 0.45
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.99
mmpR5 779243 p.Val85Gly missense_variant 0.43
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407415 c.-75T>G upstream_gene_variant 0.62
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 0.99
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169169 p.Leu482Val missense_variant 0.46
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288730 p.Ala171Gly missense_variant 0.59
pncA 2289211 p.Asn11His missense_variant 0.46
pncA 2289216 p.Val9Pro missense_variant 0.43
ribD 2986827 c.-12G>A upstream_gene_variant 0.52
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449256 c.753G>A synonymous_variant 0.37
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 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326323 p.Val384Ala missense_variant 0.65
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