TB-Profiler result

Run: ERR8025731
Summary

Run ID: ERR8025731

Sample name:

Date: 18-05-2023 07:15:17

Number of reads: 2504443

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 c.351delG (0.10), gid p.Leu79Ser (1.00)
Fluoroquinolones R gyrA p.Asp94Tyr (0.91)
Moxifloxacin R gyrA p.Asp94Tyr (0.91)
Ofloxacin R gyrA p.Asp94Tyr (0.91)
Levofloxacin R gyrA p.Asp94Tyr (0.91)
Ciprofloxacin R gyrA p.Asp94Tyr (0.91)
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 7581 p.Asp94Tyr missense_variant 0.91 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 4407851 c.351delG frameshift_variant 0.1 streptomycin
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 9045 p.Tyr582His missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491662 p.Val294Ile missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760876 p.Val357Ala missense_variant 0.12
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
fbiC 1303485 c.555C>A synonymous_variant 0.12
fbiC 1303658 p.Arg243His missense_variant 0.14
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
ndh 2102374 c.668dupC frameshift_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156095 p.Pro6Gln missense_variant 0.13
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
kasA 2518890 p.Ala259Asp missense_variant 0.12
eis 2714889 c.444C>T synonymous_variant 0.12
folC 2746566 p.Ala345Thr missense_variant 0.13
folC 2747413 c.186C>T synonymous_variant 0.13
ribD 2987433 p.Leu199Ile missense_variant 0.11
Rv2752c 3066351 c.-160G>A upstream_gene_variant 0.11
thyX 3067212 p.Pro245Gln missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339678 c.561C>T synonymous_variant 0.16
Rv3083 3449216 p.Trp238Leu missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474072 p.Leu22Phe missense_variant 0.12
fprA 3474989 p.Pro328His missense_variant 0.14
Rv3236c 3612625 c.492C>A synonymous_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641757 p.Arg75Ser missense_variant 0.12
alr 3841200 p.Ala74Asp missense_variant 0.11
clpC1 4039243 p.Leu488Val missense_variant 0.11
clpC1 4039352 c.1353C>A synonymous_variant 0.14
embC 4242587 p.Gly909Arg missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243095 p.Gly1078Glu missense_variant 0.11
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243603 p.Ala124Val missense_variant 0.15
embA 4243897 p.Ala222Val missense_variant 0.13
embB 4249055 p.Tyr848Asn missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268055 p.Asn261Ser missense_variant 0.12
ethR 4328161 p.His205Asn missense_variant 0.14
ethA 4328226 c.-753G>A upstream_gene_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