TB-Profiler result

Run: SRR25827576
Summary

Run ID: SRR25827576

Sample name:

Date: 21-03-2024 13:42:09

Number of reads: 6781741

Percentage reads mapped: 99.12

Strain: lineage2.2.1

Drug-resistance: MDR-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)
Isoniazid R fabG1 c.-8T>A (0.53), inhA c.-154G>A (0.46), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Ala28Asp (0.53), pncA c.-11A>G (0.48)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides R rrs n.1401A>G (0.52)
Amikacin R rrs n.1401A>G (0.52)
Capreomycin R rrs n.1401A>G (0.52)
Kanamycin R rrs n.1401A>G (0.52)
Cycloserine
Ethionamide R inhA c.-154G>A (0.46)
Clofazimine
Para-aminosalicylic_acid R folC p.Ile43Thr (0.55)
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.52 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673432 c.-8T>A upstream_gene_variant 0.53 isoniazid
inhA 1674048 c.-154G>A upstream_gene_variant 0.46 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289159 p.Ala28Asp missense_variant 0.53 pyrazinamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.48 pyrazinamide
folC 2747471 p.Ile43Thr missense_variant 0.55 para-aminosalicylic_acid
embB 4247429 p.Met306Val 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 8164 p.Ala288Asp missense_variant 0.47
gyrA 9128 c.1827C>A synonymous_variant 0.47
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.5
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.5
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761268 p.Ile488Val missense_variant 0.49
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 767123 p.Val1252Leu missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.52
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
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 2154242 p.Met624Val missense_variant 0.53
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
eis 2714629 p.Leu235Arg missense_variant 0.53
thyA 3073682 c.789_790insG frameshift_variant 0.48
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 0.99
embC 4241022 p.Ala387Val missense_variant 0.5
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 0.18
embB 4248353 p.Val614Ile missense_variant 0.5
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269299 p.Ile179Val missense_variant 0.47
ethA 4326676 p.Ser266Arg missense_variant 0.5
ethA 4327344 p.Thr44Ala missense_variant 0.53
ethA 4327409 p.His22Arg missense_variant 0.48
whiB6 4338229 p.Leu98Arg missense_variant 0.49
whiB6 4338266 p.Arg86Trp missense_variant 0.46
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 4407927 p.Glu92Asp missense_variant 1.0