TB-Profiler result

Run: SRR24256084

Summary

Run ID: SRR24256084

Sample name:

Date: 22-01-2024 12:49:10

Number of reads: 5351044

Percentage reads mapped: 99.58

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-TB


Download CSV Download TXT Download PDF Download JSON
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.Asp485Asn (0.46)
Isoniazid R katG p.Ile335Val (0.41), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (0.51), embB p.Gln497Arg (0.41)
Pyrazinamide R pncA p.Gln141Pro (0.60), pncA p.Ile6Ser (0.47)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrA p.Ala90Val (0.66), gyrA p.Asp94Gly (0.35)
Moxifloxacin R gyrA p.Ala90Val (0.66), gyrA p.Asp94Gly (0.35)
Ofloxacin R gyrA p.Ala90Val (0.66), gyrA p.Asp94Gly (0.35)
Levofloxacin R gyrA p.Ala90Val (0.66), gyrA p.Asp94Gly (0.35)
Ciprofloxacin R gyrA p.Ala90Val (0.66), gyrA p.Asp94Gly (0.35)
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 ethA c.884delT (0.50), ethA c.884delT (0.50)
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
gyrA 7570 p.Ala90Val missense_variant 0.66 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.35 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764822 p.Asp485Asn missense_variant 0.46 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
katG 2155109 p.Ile335Val missense_variant 0.41 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288820 p.Gln141Pro missense_variant 0.6 pyrazinamide
pncA 2289225 p.Ile6Ser missense_variant 0.47 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.51 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.41 ethambutol
ethA 4326589 c.884delT frameshift_variant 0.5 ethionamide, 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 0.56
ccsA 620625 p.Ile245Met missense_variant 0.48
rpoB 761293 p.Val496Ala missense_variant 0.56
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.61
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302917 c.-14_-13insA upstream_gene_variant 0.47
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
rpsA 1834776 p.Ala412Val missense_variant 0.45
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 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086731 c.-89A>G upstream_gene_variant 0.47
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
fbiB 3640879 c.-656C>T upstream_gene_variant 0.46
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.53
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243598 c.366G>A synonymous_variant 0.47
embB 4247872 c.1359C>T synonymous_variant 0.42
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326474 p.Pro334Ala missense_variant 0.5
ethA 4327418 p.Ala19Glu missense_variant 0.51
whiB6 4338326 p.Ala66Thr missense_variant 0.41
whiB6 4338371 p.Thr51Pro missense_variant 0.56
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