TB-Profiler result

Run: SRR25827641

Summary

Run ID: SRR25827641

Sample name:

Date: 02-02-2024 13:02:40

Number of reads: 11867838

Percentage reads mapped: 99.14

Strain: lineage4;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 (0.96)
Isoniazid R katG p.Ser315Thr (0.97)
Ethambutol R embA c.-11C>A (0.38), embB p.Met306Val (0.55), embB p.Gly406Ser (0.17)
Pyrazinamide R pncA p.Leu27Pro (0.45), pncA c.-11A>G (0.13)
Streptomycin R rpsL p.Lys43Arg (0.86), rpsL p.Lys88Thr (0.14)
Fluoroquinolones R gyrA p.Ala90Val (0.16), gyrA p.Ser91Pro (0.24), gyrA p.Asp94Gly (0.47)
Moxifloxacin R gyrA p.Ala90Val (0.16), gyrA p.Ser91Pro (0.24), gyrA p.Asp94Gly (0.47)
Ofloxacin R gyrA p.Ala90Val (0.16), gyrA p.Ser91Pro (0.24), gyrA p.Asp94Gly (0.47)
Levofloxacin R gyrA p.Ala90Val (0.16), gyrA p.Ser91Pro (0.24), gyrA p.Asp94Gly (0.47)
Ciprofloxacin R gyrA p.Ala90Val (0.16), gyrA p.Ser91Pro (0.24), gyrA p.Asp94Gly (0.47)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.13)
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.81
lineage4 Euro-American LAM;T;S;X;H None 0.08
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.81
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.81
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 0.16 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.24 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.47 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.96 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.86 streptomycin
rpsL 781822 p.Lys88Thr missense_variant 0.14 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.13 linezolid
katG 2155168 p.Ser315Thr missense_variant 0.97 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 0.45 pyrazinamide
pncA 2289252 c.-11A>G upstream_gene_variant 0.13 pyrazinamide
embA 4243222 c.-11C>A upstream_gene_variant 0.38 ethambutol
embB 4247429 p.Met306Val missense_variant 0.55 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.17 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 9304 p.Gly668Asp missense_variant 0.99
fgd1 491290 p.Val170Met missense_variant 0.33
fgd1 491742 c.960T>C synonymous_variant 0.91
mshA 575907 p.Ala187Val missense_variant 0.4
ccsA 620625 p.Ile245Met missense_variant 0.83
rpoB 761557 p.Ala584Asp missense_variant 0.16
rpoC 763031 c.-339T>C upstream_gene_variant 0.93
rpoC 766488 p.Pro1040Arg missense_variant 0.34
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.94
mmpL5 776182 p.Asp767Asn missense_variant 0.42
mmpS5 779615 c.-710C>G upstream_gene_variant 0.78
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.79
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.79
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.91
PPE35 2167926 p.Leu896Ser missense_variant 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288758 p.Gly162Arg missense_variant 0.12
pncA 2289513 c.-272G>A upstream_gene_variant 0.45
ribD 2986827 c.-12G>A upstream_gene_variant 0.17
Rv2752c 3066004 p.Asp63Ala missense_variant 0.2
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 0.79
embC 4241022 p.Ala387Val missense_variant 0.35
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.8
aftB 4267647 p.Asp397Gly missense_variant 0.8
ubiA 4269311 p.Trp175Gly missense_variant 0.16
ethA 4326676 p.Ser266Arg missense_variant 0.41
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.9
gid 4407620 p.Tyr195His missense_variant 0.33
gid 4407927 p.Glu92Asp missense_variant 0.83