TB-Profiler result

Run: ERR4809359

Summary

Run ID: ERR4809359

Sample name:

Date: 20-10-2023 15:54:41

Number of reads: 2711825

Percentage reads mapped: 99.66

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.Gln429Leu (1.00), rpoB p.Asp435Tyr (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.Tyr34* (1.00)
Streptomycin R gid p.Leu79Ser (1.00)
Fluoroquinolones R gyrB p.Arg446Leu (1.00), gyrA p.Asp89Asn (0.18), gyrA p.Asp94Gly (0.71)
Moxifloxacin R gyrB p.Arg446Leu (1.00), gyrA p.Asp89Asn (0.18), gyrA p.Asp94Gly (0.71)
Ofloxacin R gyrB p.Arg446Leu (1.00), gyrA p.Asp89Asn (0.18), gyrA p.Asp94Gly (0.71)
Levofloxacin R gyrB p.Arg446Leu (1.00), gyrA p.Asp89Asn (0.18), gyrA p.Asp94Gly (0.71)
Ciprofloxacin R gyrB p.Arg446Leu (1.00), gyrA p.Asp89Asn (0.18), gyrA p.Asp94Gly (0.71)
Aminoglycosides R rrs n.1484G>T (1.00)
Amikacin R rrs n.1484G>T (1.00)
Capreomycin R rrs n.1484G>T (1.00)
Kanamycin R rrs n.1484G>T (1.00)
Cycloserine
Ethionamide R ethA p.Ala381Pro (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 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 6576 p.Arg446Leu missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7566 p.Asp89Asn missense_variant 0.18 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.71 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761092 p.Gln429Leu missense_variant 1.0 rifampicin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289140 p.Tyr34* stop_gained 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 1.0 ethionamide
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin
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
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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801270 c.463_465dupGCC conservative_inframe_insertion 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674685 p.Thr162Ser missense_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 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly 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 1.0