TB-Profiler result

Run: SRR25827562

Summary

Run ID: SRR25827562

Sample name:

Date: 15-02-2024 06:18:04

Number of reads: 9493849

Percentage reads mapped: 99.04

Strain: lineage4.2.2.2;lineage2.2.1

Drug-resistance: Pre-XDR-TB


Download CSV Download TXT Download PDF Download JSON
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), rpoB p.Ile480Val (0.18)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.85)
Pyrazinamide R pncA p.Leu27Pro (0.83)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrB p.Arg446His (0.73)
Moxifloxacin R gyrB p.Arg446His (0.73)
Ofloxacin R gyrB p.Arg446His (0.73)
Levofloxacin R gyrB p.Arg446His (0.73)
Ciprofloxacin R gyrB p.Arg446His (0.73)
Aminoglycosides R rrs n.1401A>G (0.80)
Amikacin R rrs n.1401A>G (0.80)
Capreomycin R rrs n.1401A>G (0.80)
Kanamycin R rrs n.1401A>G (0.80)
Cycloserine
Ethionamide
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 0.82
lineage4 Euro-American LAM;T;S;X;H None 0.16
lineage4.2 Euro-American H;T;LAM None 0.18
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.82
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.18
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.83
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.19
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
gyrB 6576 p.Arg446His missense_variant 0.73 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoB 761244 p.Ile480Val missense_variant 0.18 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.8 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 0.83 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.85 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 0.82
mshA 576077 c.730C>T synonymous_variant 0.21
mshA 576453 p.Val369Gly missense_variant 0.23
mshA 576651 p.Asp435Ala missense_variant 0.19
ccsA 620625 p.Ile245Met missense_variant 0.84
rpoC 763031 c.-339T>C upstream_gene_variant 0.88
rpoC 766488 p.Pro1040Arg missense_variant 0.85
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.79
mmpS5 779615 c.-710C>G upstream_gene_variant 0.88
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.85
atpE 1461231 p.Ala63Pro missense_variant 0.91
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.79
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.79
PPE35 2167926 p.Leu896Ser missense_variant 0.75
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 0.19
Rv2752c 3065298 c.894C>T synonymous_variant 0.81
ald 3086742 c.-78A>C upstream_gene_variant 0.19
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 0.82
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.8
embA 4245835 p.Leu868Arg missense_variant 0.17
embB 4247015 p.Ser168Ala missense_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 0.71
ethA 4326676 p.Ser266Arg missense_variant 0.81
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.91
gid 4407927 p.Glu92Asp missense_variant 0.85