TB-Profiler result

Run: SRR25827572
Summary

Run ID: SRR25827572

Sample name:

Date: 21-03-2024 13:22:05

Number of reads: 3867201

Percentage reads mapped: 49.81

Strain: lineage4.1.1.3;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.Ser450Leu (0.60)
Isoniazid R fabG1 c.-15C>T (0.57), katG p.Ser315Thr (0.46)
Ethambutol R embB p.Met306Val (0.52)
Pyrazinamide R pncA p.Thr177Pro (0.46)
Streptomycin R rpsL p.Lys43Arg (0.52)
Fluoroquinolones R gyrA p.Asp94Gly (0.44)
Moxifloxacin R gyrA p.Asp94Gly (0.44)
Ofloxacin R gyrA p.Asp94Gly (0.44)
Levofloxacin R gyrA p.Asp94Gly (0.44)
Ciprofloxacin R gyrA p.Asp94Gly (0.44)
Aminoglycosides R rrs n.1401A>G (0.48)
Amikacin R rrs n.1401A>G (0.48)
Capreomycin R rrs n.1401A>G (0.48)
Kanamycin R rrs n.1401A>G (0.48)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.57), ethA c.774dupG (0.37), ethA c.774dupG (0.37)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.48)
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 0.45
lineage4 Euro-American LAM;T;S;X;H None 0.59
lineage4.1 Euro-American T;X;H None 0.54
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.46
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.42
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.56
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.57
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 0.44 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.6 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.52 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.48 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.57 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.46 isoniazid
pncA 2288713 p.Thr177Pro missense_variant 0.46 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.48 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.52 ethambutol
ethA 4326699 c.774dupG frameshift_variant 0.37 ethionamide, 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 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.43
mshA 575907 p.Ala187Val missense_variant 0.5
ccsA 620625 p.Ile245Met missense_variant 0.39
rpoB 759694 c.-113C>T upstream_gene_variant 0.63
rpoC 763031 c.-339T>C upstream_gene_variant 0.52
rpoC 764840 p.Ile491Val missense_variant 0.48
rpoC 765150 p.Gly594Glu missense_variant 0.63
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.4
mmpL5 776182 p.Asp767Asn missense_variant 0.45
mmpS5 779615 c.-710C>G upstream_gene_variant 0.46
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.36
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
rpsA 1834177 c.636A>C synonymous_variant 0.41
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.41
PPE35 2167926 p.Leu896Ser missense_variant 0.39
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449354 c.852dupC frameshift_variant 0.46
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.44
embC 4241022 p.Ala387Val missense_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.62
embA 4243460 c.228C>T synonymous_variant 0.47
embB 4247028 p.Leu172Arg missense_variant 0.24
embB 4249408 c.2895G>A synonymous_variant 0.53
aftB 4267463 c.1374C>T synonymous_variant 0.53
aftB 4267647 p.Asp397Gly missense_variant 0.43
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.39
gid 4407620 p.Tyr195His missense_variant 0.41
gid 4407927 p.Glu92Asp missense_variant 0.48