TB-Profiler result

Run: SRR25827371

Summary

Run ID: SRR25827371

Sample name:

Date: 01-02-2024 04:30:20

Number of reads: 9307229

Percentage reads mapped: 99.22

Strain: lineage4.8;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 (0.62)
Isoniazid R fabG1 c.-15C>T (0.51), katG p.Ser315Thr (0.53)
Ethambutol R embB p.Gln497Arg (0.60)
Pyrazinamide R pncA p.Gly132Ala (0.53)
Streptomycin R rpsL p.Lys43Arg (0.55)
Fluoroquinolones R gyrA p.Ala90Val (0.57)
Moxifloxacin R gyrA p.Ala90Val (0.57)
Ofloxacin R gyrA p.Ala90Val (0.57)
Levofloxacin R gyrA p.Ala90Val (0.57)
Ciprofloxacin R gyrA p.Ala90Val (0.57)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-10G>C (0.60), eis c.-10G>C (0.60)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.51)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.60)
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 0.57
lineage4 Euro-American LAM;T;S;X;H None 0.44
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.57
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.44
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.54
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 0.57 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.62 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.55 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.51 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.53 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.53 pyrazinamide
eis 2715342 c.-10G>C upstream_gene_variant 0.6 kanamycin, kanamycin
thyX 3067961 c.-16C>T upstream_gene_variant 0.6 para-aminosalicylic_acid
embB 4248003 p.Gln497Arg missense_variant 0.6 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 0.57
gyrA 9304 p.Gly668Asp missense_variant 0.59
fgd1 491290 p.Val170Met missense_variant 0.65
fgd1 491742 c.960T>C synonymous_variant 0.55
mshA 575907 p.Ala187Val missense_variant 0.59
ccsA 620625 p.Ile245Met missense_variant 0.59
rpoC 763031 c.-339T>C upstream_gene_variant 0.56
rpoC 764840 p.Ile491Val missense_variant 0.58
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.6
mmpL5 776182 p.Asp767Asn missense_variant 0.61
mmpS5 779615 c.-710C>G upstream_gene_variant 0.52
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.53
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.52
rpsA 1834177 c.636A>C synonymous_variant 0.52
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.53
PPE35 2167926 p.Leu896Ser missense_variant 0.59
PPE35 2168149 p.Pro822Ser missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.58
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.59
Rv3236c 3612813 p.Thr102Ala missense_variant 0.55
clpC1 4039729 p.Asp326Asn missense_variant 0.43
embC 4241022 p.Ala387Val missense_variant 0.57
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.54
embB 4247028 p.Leu172Arg missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 0.6
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.59
gid 4407620 p.Tyr195His missense_variant 0.61
gid 4407927 p.Glu92Asp missense_variant 0.54