TB-Profiler result

Run: SRR24112527
Summary

Run ID: SRR24112527

Sample name:

Date: 16-04-2023 20:35:09

Number of reads: 5409462

Percentage reads mapped: 99.54

Strain: lineage2.2.2

Drug-resistance: MDR-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.His445Leu (0.98)
Isoniazid R katG c.375_382dupCATGCAGC (0.24)
Ethambutol
Pyrazinamide R pncA c.-11A>C (0.94)
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.264delC (0.99)
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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.97
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
rpoB 761140 p.His445Leu missense_variant 0.98 rifampicin
katG 2155729 c.375_382dupCATGCAGC frameshift_variant 0.24 isoniazid
pncA 2289252 c.-11A>C upstream_gene_variant 0.94 pyrazinamide
ethA 4327209 c.264delC frameshift_variant 0.99 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
gyrB 5080 c.-160_-159insGA upstream_gene_variant 0.99
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
fbiC 1305026 p.Glu699Gly missense_variant 0.95
Rv1258c 1406145 p.Ala399Val missense_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155417 p.Pro232Leu missense_variant 0.23
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289374 c.-133T>G upstream_gene_variant 0.94
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 1.0
rpoA 3878567 c.-60C>G upstream_gene_variant 0.14
embC 4240385 p.Pro175Ala missense_variant 0.95
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243222 c.-11C>T upstream_gene_variant 0.99
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.18
embB 4246548 p.Pro12Gln missense_variant 0.19
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.19
embB 4246563 p.Leu17Trp missense_variant 0.22
embB 4246567 c.54G>T synonymous_variant 0.22
embB 4247573 p.Asp354Asn missense_variant 0.92
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4326130 c.1344G>A synonymous_variant 0.98
whiB6 4338289 p.Gly78Ala missense_variant 0.99
whiB6 4338480 c.42T>C synonymous_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4407931 p.Leu91Pro missense_variant 0.98