TB-Profiler result

Run: ERR4800599

Summary

Run ID: ERR4800599

Sample name:

Date: 20-10-2023 04:28:08

Number of reads: 7227910

Percentage reads mapped: 99.5

Strain: lineage2.2.1

Drug-resistance: 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 (0.99), rpoC p.Ile491Thr (0.99)
Isoniazid R katG p.Ser315Thr (0.99)
Ethambutol R embA c.-16C>T (0.98)
Pyrazinamide R pncA p.Ile5Ser (0.99)
Streptomycin R rpsL p.Lys43Arg (0.99)
Fluoroquinolones R gyrA p.Ser91Pro (0.99)
Moxifloxacin R gyrA p.Ser91Pro (0.99)
Ofloxacin R gyrA p.Ser91Pro (0.99)
Levofloxacin R gyrA p.Ser91Pro (0.99)
Ciprofloxacin R gyrA p.Ser91Pro (0.99)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (0.99)
Cycloserine
Ethionamide R ethA c.311delT (0.26)
Clofazimine
Para-aminosalicylic_acid R thyA p.Thr22Ala (0.99)
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.73)
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.99 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.73 linezolid
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289228 p.Ile5Ser missense_variant 0.99 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.99 kanamycin
thyA 3074408 p.Thr22Ala missense_variant 0.99 para-aminosalicylic_acid
embA 4243217 c.-16C>T upstream_gene_variant 0.98 ethambutol
ethA 4327162 c.311delT frameshift_variant 0.26 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 0.98
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.99
ccsA 620625 p.Ile245Met missense_variant 0.99
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475927 n.2270G>T non_coding_transcript_exon_variant 0.19
rpsA 1834177 c.636A>C synonymous_variant 0.98
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
thyX 3067949 c.-4C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
Rv3236c 3612813 p.Thr102Ala missense_variant 0.98
rpoA 3878637 c.-130G>C upstream_gene_variant 0.21
embC 4241022 p.Ala387Val missense_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.99
embB 4247847 p.Gln445Arg missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 0.98
ethA 4326041 p.Leu478Arg missense_variant 0.74
whiB6 4338292 p.Ala77Val missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0