TB-Profiler result

Run: SRR671855
Summary

Run ID: SRR671855

Sample name:

Date: 20-10-2023 21:50:23

Number of reads: 6030922

Percentage reads mapped: 99.51

Strain: lineage2.2.2

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 (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Gln497Pro (1.00)
Pyrazinamide R pncA p.Gln141Pro (1.00)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.756dupC (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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.95
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 1.0
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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288820 p.Gln141Pro missense_variant 1.0 pyrazinamide
embB 4248003 p.Gln497Pro missense_variant 1.0 ethambutol
ethA 4326717 c.756dupC frameshift_variant 1.0 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 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 1.0
rpoB 759939 p.Pro45Ser missense_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
mmpL5 776356 p.Leu709Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406276 c.1065G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170487 c.126T>C synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289469 c.-228C>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474851 p.Arg282Leu missense_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641137 p.Ala199Thr missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246662 p.Val50Ala missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267764 p.Pro358Leu missense_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408182 c.21G>A synonymous_variant 1.0
Rv1979c 2217878 c.746_*3840del frameshift_variant&stop_lost&splice_region_variant 1.0
whiB6 4337383 c.-189_*787del transcript_ablation 1.0