TB-Profiler result

Run: ERR8025484
Summary

Run ID: ERR8025484

Sample name:

Date: 17-05-2023 23:20:12

Number of reads: 3096237

Percentage reads mapped: 99.7

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.Asp357Asn (0.29), 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.Asp94Asn (1.00)
Moxifloxacin R gyrA p.Asp94Asn (1.00)
Ofloxacin R gyrA p.Asp94Asn (1.00)
Levofloxacin R gyrA p.Asp94Asn (1.00)
Ciprofloxacin R gyrA p.Asp94Asn (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 7581 p.Asp94Asn 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 2155043 p.Asp357Asn missense_variant 0.29 isoniazid
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
gyrB 7199 p.Glu654Lys missense_variant 0.22
gyrB 7257 p.Leu673Gln missense_variant 0.17
gyrA 7342 p.Arg14Leu missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9328 p.Ala676Asp missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491772 c.990C>A synonymous_variant 0.15
mshA 575397 p.Arg17His missense_variant 0.13
mshA 575498 p.Ala51Ser missense_variant 0.13
rpoB 760496 c.690G>A synonymous_variant 0.15
rpoB 760949 c.1143C>T synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764584 c.1215G>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776338 p.Ala715Ser missense_variant 0.18
mmpL5 776914 p.Leu523Val missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1461086 c.42A>G synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472107 n.262A>G non_coding_transcript_exon_variant 0.18
rrl 1474789 n.1137delC non_coding_transcript_exon_variant 0.29
rrl 1476055 n.2398C>T non_coding_transcript_exon_variant 0.33
fabG1 1673485 p.Arg16Ser missense_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834286 p.Ser249Thr missense_variant 0.11
rpsA 1834604 p.Arg355Cys missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102504 p.Pro180His missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155004 p.Gly370Trp missense_variant 0.18
katG 2155139 p.Pro325Thr missense_variant 0.15
katG 2155737 c.375C>T synonymous_variant 0.13
katG 2156093 p.Pro7Ser missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168904 p.Ile570Thr missense_variant 0.17
PPE35 2169823 p.Ala264Thr missense_variant 0.18
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289667 c.-426C>T upstream_gene_variant 0.12
kasA 2517965 c.-150C>A upstream_gene_variant 0.12
kasA 2518005 c.-110A>T upstream_gene_variant 0.14
thyA 3074103 c.369C>A synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086821 c.2T>C start_lost 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4040754 c.-50C>A upstream_gene_variant 0.12
clpC1 4040760 c.-56C>T upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245479 p.Met749Ile missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268022 p.Leu272Gln missense_variant 0.12
ethA 4326184 c.1290C>A synonymous_variant 0.11
ethA 4326422 p.Gly351Val missense_variant 0.33
ethR 4327672 p.Leu42Met missense_variant 0.2
ethR 4327682 p.Ile45Asn missense_variant 0.2
ethR 4327781 p.Arg78Gln missense_variant 0.13
ethA 4328115 c.-642G>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