TB-Profiler result

Run: SRR25827802
Summary

Run ID: SRR25827802

Sample name:

Date: 02-02-2024 19:55:59

Number of reads: 6160530

Percentage reads mapped: 99.14

Strain: lineage4.3;lineage2.2.1

Drug-resistance: Pre-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.Asp435Val (0.36), rpoB p.Ser450Leu (0.67)
Isoniazid R fabG1 c.-15C>T (1.00)
Ethambutol R embA c.-11C>A (0.65), embB p.Met306Val (1.00)
Pyrazinamide R pncA c.187_188insT (0.39), pncA p.Leu27Pro (0.57)
Streptomycin R rpsL p.Lys43Arg (0.61)
Fluoroquinolones R gyrA p.Ala90Val (1.00)
Moxifloxacin R gyrA p.Ala90Val (1.00)
Ofloxacin R gyrA p.Ala90Val (1.00)
Levofloxacin R gyrA p.Ala90Val (1.00)
Ciprofloxacin R gyrA p.Ala90Val (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00)
Clofazimine
Para-aminosalicylic_acid
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 0.6
lineage4 Euro-American LAM;T;S;X;H None 0.39
lineage4.3 Euro-American (LAM) mainly-LAM None 0.36
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.62
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.6
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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.36 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.67 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.61 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2289054 c.187_188insT frameshift_variant 0.39 pyrazinamide
pncA 2289162 p.Leu27Pro missense_variant 0.57 pyrazinamide
embA 4243222 c.-11C>A upstream_gene_variant 0.65 ethambutol
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.59
ccsA 620625 p.Ile245Met missense_variant 0.6
rpoC 763031 c.-339T>C upstream_gene_variant 0.61
rpoC 764995 c.1626C>G synonymous_variant 0.31
rpoC 766488 p.Pro1040Arg missense_variant 0.62
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.58
mmpS5 779615 c.-710C>G upstream_gene_variant 0.6
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.63
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472920 n.1077dupT non_coding_transcript_exon_variant 0.29
rpsA 1834177 c.636A>C synonymous_variant 0.58
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.69
katG 2155168 p.Ser315Ala missense_variant 0.63
PPE35 2167926 p.Leu896Ser missense_variant 0.63
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746932 p.Ala223Thr missense_variant 0.33
thyA 3073868 p.Thr202Ala missense_variant 0.44
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568418 c.250_261delGGACGTCCGCGC conservative_inframe_deletion 0.8
whiB7 3568854 c.-176delG upstream_gene_variant 0.51
Rv3236c 3612813 p.Thr102Ala missense_variant 0.54
clpC1 4038287 c.2418C>T synonymous_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.63
embB 4247028 p.Leu172Arg missense_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 0.61
ethA 4326513 p.Thr321Pro missense_variant 0.69
ethA 4326676 p.Ser266Arg missense_variant 0.64
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.61
gid 4407927 p.Glu92Asp missense_variant 0.57
gid 4408156 p.Leu16Arg missense_variant 0.37