TB-Profiler result

Run: SRR25827601
Summary

Run ID: SRR25827601

Sample name:

Date: 21-03-2024 14:49:20

Number of reads: 14938158

Percentage reads mapped: 99.24

Strain: lineage2.2.1.1

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 (1.00), rpoC p.Ile491Thr (0.67)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embA c.-16C>T (0.67)
Pyrazinamide R pncA p.Ile5Ser (0.68), pncA p.Ala3Glu (0.22)
Streptomycin R rpsL p.Lys43Arg (0.83), rpsL p.Lys88Arg (0.21)
Fluoroquinolones R gyrA p.Ala90Val (0.13), gyrA p.Asp94Ala (0.19), gyrA p.Asp94Gly (0.68)
Moxifloxacin R gyrA p.Ala90Val (0.13), gyrA p.Asp94Ala (0.19), gyrA p.Asp94Gly (0.68)
Ofloxacin R gyrA p.Ala90Val (0.13), gyrA p.Asp94Ala (0.19), gyrA p.Asp94Gly (0.68)
Levofloxacin R gyrA p.Ala90Val (0.13), gyrA p.Asp94Ala (0.19), gyrA p.Asp94Gly (0.68)
Ciprofloxacin R gyrA p.Ala90Val (0.13), gyrA p.Asp94Ala (0.19), gyrA p.Asp94Gly (0.68)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (0.71)
Cycloserine
Ethionamide R ethA p.Tyr84Asp (0.24)
Clofazimine
Para-aminosalicylic_acid R thyA p.Thr22Ala (0.64)
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.69)
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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.21
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 0.13 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.19 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.68 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.67 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.83 streptomycin
rpsL 781822 p.Lys88Arg missense_variant 0.21 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.69 linezolid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289228 p.Ile5Ser missense_variant 0.68 pyrazinamide
pncA 2289234 p.Ala3Glu missense_variant 0.22 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.71 kanamycin
thyA 3074408 p.Thr22Ala missense_variant 0.64 para-aminosalicylic_acid
embA 4243217 c.-16C>T upstream_gene_variant 0.67 ethambutol
ethA 4327224 p.Tyr84Asp missense_variant 0.24 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 0.67
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.9
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764363 p.Gly332Ser missense_variant 0.22
rpoC 764669 p.Pro434Ser missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.89
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 0.12
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 0.16
eis 2714846 p.Val163Ile missense_variant 0.2
thyX 3067949 c.-4C>T upstream_gene_variant 0.7
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
embC 4241022 p.Ala387Val missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 0.2
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.14
embB 4247847 p.Gln445Arg missense_variant 0.69
embB 4247861 p.Ile450Leu missense_variant 0.18
embB 4248115 c.1602C>T synonymous_variant 0.2
embB 4248353 p.Val614Ile missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326676 p.Ser266Arg missense_variant 0.13
ethA 4327283 p.Phe64Cys missense_variant 0.64
ethA 4327344 p.Thr44Ala missense_variant 0.13
whiB6 4338292 p.Ala77Val missense_variant 0.63
whiB6 4338365 p.Cys53Arg missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 0.71
gid 4407732 c.471G>A synonymous_variant 0.2
gid 4407927 p.Glu92Asp missense_variant 1.0