TB-Profiler result

Run: ERR4798998

Summary

Run ID: ERR4798998

Sample name:

Date: 20-10-2023 03:19:41

Number of reads: 3813488

Percentage reads mapped: 99.63

Strain: lineage3;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 (0.62)
Isoniazid R katG p.Ser315Thr (0.55)
Ethambutol R embB p.Gln497Arg (0.47)
Pyrazinamide R pncA p.Cys138Arg (0.53)
Streptomycin R rpsL p.Lys43Arg (0.47)
Fluoroquinolones R gyrA p.Ser91Pro (0.53)
Moxifloxacin R gyrA p.Ser91Pro (0.53)
Ofloxacin R gyrA p.Ser91Pro (0.53)
Levofloxacin R gyrA p.Ser91Pro (0.53)
Ciprofloxacin R gyrA p.Ser91Pro (0.53)
Aminoglycosides R rrs n.1401A>G (0.51)
Amikacin R rrs n.1401A>G (0.51)
Capreomycin R rrs n.1401A>G (0.51)
Kanamycin R rrs n.1401A>G (0.51)
Cycloserine
Ethionamide R ethA p.Ser57Tyr (0.52)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.51
lineage2 East-Asian Beijing RD105 0.51
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.51
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.51
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 7572 p.Ser91Pro missense_variant 0.53 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.62 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.47 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.51 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.55 isoniazid
pncA 2288830 p.Cys138Arg missense_variant 0.53 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.47 ethambutol
ethA 4327304 p.Ser57Tyr missense_variant 0.52 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 491290 p.Val170Met missense_variant 0.65
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.56
ccsA 620625 p.Ile245Met missense_variant 0.44
rpoB 759746 c.-61C>T upstream_gene_variant 0.46
rpoC 762434 c.-936T>G upstream_gene_variant 0.53
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764533 c.1164C>A synonymous_variant 0.72
rpoC 764840 p.Ile491Val missense_variant 0.43
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.49
mmpS5 779615 c.-710C>G upstream_gene_variant 0.55
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.45
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473165 n.1320C>T non_coding_transcript_exon_variant 0.61
rpsA 1834177 c.636A>C synonymous_variant 0.37
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
pncA 2289365 c.-125delC upstream_gene_variant 0.43
ahpC 2726105 c.-88G>A upstream_gene_variant 0.43
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.52
fbiB 3642877 p.Lys448Arg missense_variant 0.54
embC 4241022 p.Ala387Val missense_variant 0.49
embC 4242075 p.Arg738Gln missense_variant 0.59
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.48
embA 4246255 p.Leu1008Pro missense_variant 0.46
aftB 4267647 p.Asp397Gly missense_variant 0.59
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.51
gid 4407790 p.Ala138Val missense_variant 0.42
gid 4407927 p.Glu92Asp missense_variant 0.55