TB-Profiler result

Run: SRR25827503

Summary

Run ID: SRR25827503

Sample name:

Date: 02-02-2024 06:09:18

Number of reads: 7271698

Percentage reads mapped: 99.28

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 p.Ser450Leu (1.00), rpoC p.Ile491Thr (0.28)
Isoniazid R fabG1 c.-15C>T (0.75), katG p.Ser315Thr (1.00)
Ethambutol R embA c.-16C>T (1.00), embB p.Gly406Ser (0.74)
Pyrazinamide R pncA c.391dupG (0.73), pncA c.391dupG (0.73), pncA p.Ile5Ser (0.27)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrA p.Asp94Ala (0.71), gyrA p.Asp94Gly (0.29)
Moxifloxacin R gyrA p.Asp94Ala (0.71), gyrA p.Asp94Gly (0.29)
Ofloxacin R gyrA p.Asp94Ala (0.71), gyrA p.Asp94Gly (0.29)
Levofloxacin R gyrA p.Asp94Ala (0.71), gyrA p.Asp94Gly (0.29)
Ciprofloxacin R gyrA p.Asp94Ala (0.71), gyrA p.Asp94Gly (0.29)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (0.26)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.75), ethA c.93dupC (0.30)
Clofazimine
Para-aminosalicylic_acid R thyA p.Thr22Ala (0.31)
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
gyrA 7582 p.Asp94Ala missense_variant 0.71 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.29 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.28 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.75 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288850 c.391dupG frameshift_variant 0.73 pyrazinamide, pyrazinamide
pncA 2289228 p.Ile5Ser missense_variant 0.27 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.26 kanamycin
thyA 3074408 p.Thr22Ala missense_variant 0.31 para-aminosalicylic_acid
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.74 ethambutol
ethA 4327380 c.93dupC frameshift_variant 0.3 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
gyrB 6529 p.Lys430Asn missense_variant 0.75
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 491290 p.Val170Met missense_variant 0.27
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 764723 p.Phe452Leu missense_variant 0.75
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779276 p.Arg96Gln missense_variant 0.2
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303326 c.396C>T synonymous_variant 0.72
Rv1258c 1406760 c.580_581insC frameshift_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
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222357 p.Thr270Ala missense_variant 0.76
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067949 c.-4C>T upstream_gene_variant 0.26
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087719 c.901_914delATGCCCGCCTCGGT frameshift_variant 0.71
fprA 3473810 c.-197A>G upstream_gene_variant 0.7
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840259 p.Tyr388Asp missense_variant 0.3
embC 4241022 p.Ala387Val missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.16
embB 4247847 p.Gln445Arg missense_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338292 p.Ala77Val missense_variant 0.29
whiB6 4338337 p.Cys62Ser missense_variant 0.69
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.29
gid 4407927 p.Glu92Asp missense_variant 1.0