TB-Profiler result

Run: ERR8025487
Summary

Run ID: ERR8025487

Sample name:

Date: 19-05-2023 16:58:58

Number of reads: 2871286

Percentage reads mapped: 99.58

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.Asp435Val (1.00)
Isoniazid R fabG1 c.-17G>T (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA c.517dupG (1.00), pncA c.517dupG (1.00)
Streptomycin R rrs n.514A>C (1.00), gid p.Leu79Ser (1.00)
Fluoroquinolones R gyrA p.Ser91Pro (1.00)
Moxifloxacin R gyrA p.Ser91Pro (1.00)
Ofloxacin R gyrA p.Ser91Pro (1.00)
Levofloxacin R gyrA p.Ser91Pro (1.00)
Ciprofloxacin R gyrA p.Ser91Pro (1.00)
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
Cycloserine
Ethionamide R fabG1 c.-17G>T (1.00), 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
gyrA 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673423 c.-17G>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288724 c.517dupG frameshift_variant 1.0 pyrazinamide, 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 7852 p.Gly184Ala missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 0.94
fgd1 491608 p.Pro276Ser missense_variant 0.13
fgd1 491651 p.Pro290His missense_variant 0.14
fgd1 491691 p.Trp303Cys missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576204 p.Ala286Val missense_variant 0.13
rpoB 761100 p.Gln432* stop_gained 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764614 c.1245G>A synonymous_variant 0.11
rpoC 765873 p.Pro835Gln missense_variant 0.12
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
rpsL 781396 c.-163delG upstream_gene_variant 0.12
embR 1417144 c.204A>G synonymous_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473022 n.1177G>T non_coding_transcript_exon_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102199 p.Ala282Thr missense_variant 0.12
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 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4242399 p.Ala846Val missense_variant 0.17
embA 4242508 c.-725G>T upstream_gene_variant 0.11
embC 4242599 p.Gly913Trp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4246799 p.Gly96Trp missense_variant 0.12
embB 4249789 c.3276C>A synonymous_variant 0.2
aftB 4267035 p.Arg601His missense_variant 0.12
aftB 4267419 p.Ala473Val missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4268971 p.Ala288Val missense_variant 0.12
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 4407942 p.Gln87His missense_variant 0.12