TB-Profiler result

Run: SRR25827543

Summary

Run ID: SRR25827543

Sample name:

Date: 02-02-2024 09:44:51

Number of reads: 7077503

Percentage reads mapped: 99.17

Strain: lineage3;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 (0.48)
Isoniazid R katG p.Ser315Thr (0.34)
Ethambutol R embB p.Met306Val (0.32)
Pyrazinamide R pncA p.Thr177Pro (0.32)
Streptomycin R rpsL p.Lys43Arg (0.33)
Fluoroquinolones R gyrA p.Asp94Gly (0.29)
Moxifloxacin R gyrA p.Asp94Gly (0.29)
Ofloxacin R gyrA p.Asp94Gly (0.29)
Levofloxacin R gyrA p.Asp94Gly (0.29)
Ciprofloxacin R gyrA p.Asp94Gly (0.29)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid R folC p.Ile43Thr (0.39)
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.41)
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.62
lineage2 East-Asian Beijing RD105 0.36
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.36
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.34
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 7582 p.Asp94Gly missense_variant 0.29 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.48 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.33 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.41 linezolid
katG 2155168 p.Ser315Thr missense_variant 0.34 isoniazid
pncA 2288713 p.Thr177Pro missense_variant 0.32 pyrazinamide
folC 2747471 p.Ile43Thr missense_variant 0.39 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.32 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 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.42
ccsA 620625 p.Ile245Met missense_variant 0.36
rpoB 759746 c.-61C>T upstream_gene_variant 0.71
rpoC 762434 c.-936T>G upstream_gene_variant 0.59
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764916 p.Leu516Pro missense_variant 0.37
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.36
mmpR5 779363 p.Leu125Pro missense_variant 0.38
mmpS5 779615 c.-710C>G upstream_gene_variant 0.35
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303326 c.396C>T synonymous_variant 0.37
Rv1258c 1406760 c.580_581insC frameshift_variant 0.31
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
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 2222357 p.Thr270Ala missense_variant 0.35
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.66
pncA 2289365 c.-125delC upstream_gene_variant 0.63
ahpC 2726105 c.-88G>A upstream_gene_variant 0.69
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473810 c.-197A>G upstream_gene_variant 0.35
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
Rv3236c 3612813 p.Thr102Ala missense_variant 0.43
embC 4242075 p.Arg738Gln missense_variant 0.65
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.37
embB 4247496 p.Asp328Ala missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 0.17
aftB 4268094 p.Asp248Gly missense_variant 0.63
ethA 4327968 c.-495C>T upstream_gene_variant 0.61
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.39