TB-Profiler result

Run: SRR25207180
Summary

Run ID: SRR25207180

Sample name:

Date: 12-02-2024 18:30:14

Number of reads: 5823733

Percentage reads mapped: 99.63

Strain: lineage2.2.2

Drug-resistance: 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
Pyrazinamide
Streptomycin
Fluoroquinolones R gyrB p.Thr500Asn (1.00), gyrA p.Asp94Ala (1.00)
Moxifloxacin R gyrB p.Thr500Asn (1.00), gyrA p.Asp94Ala (1.00)
Ofloxacin R gyrB p.Thr500Asn (1.00), gyrA p.Asp94Ala (1.00)
Levofloxacin R gyrB p.Thr500Asn (1.00), gyrA p.Asp94Ala (1.00)
Ciprofloxacin R gyrB p.Thr500Asn (1.00), gyrA p.Asp94Ala (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.83delC (1.00), ethA c.83delC (1.00)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (1.00)
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 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
gyrB 6738 p.Thr500Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rplC 801268 p.Cys154Arg missense_variant 1.0 linezolid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ethA 4327390 c.83delC frameshift_variant 1.0 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 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
mshA 576492 c.1146delC frameshift_variant 0.44
mshA 576501 c.1155dupC frameshift_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764918 p.Val517Leu missense_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
rrl 1476750 n.3093T>G non_coding_transcript_exon_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
PPE35 2167926 p.Leu896Ser missense_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
rpoA 3878614 c.-107A>C upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.33
embB 4247033 p.Ser174Arg missense_variant 0.25
embB 4247468 p.Tyr319His missense_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269298 p.Ile179Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.99
gid 4407985 p.Gly73Glu missense_variant 1.0