TB-Profiler result

Run: ERR9806865
Summary

Run ID: ERR9806865

Sample name:

Date: 18-05-2023 17:15:13

Number of reads: 2014067

Percentage reads mapped: 99.55

Strain: lineage2.2.1

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.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA c.459_466delCAGGGTGC (1.00), pncA c.459_466delCAGGGTGC (1.00)
Streptomycin R rrs n.514A>C (1.00)
Fluoroquinolones R gyrB p.Arg446Leu (0.15), gyrA p.Asp94Gly (0.94)
Moxifloxacin R gyrB p.Arg446Leu (0.15), gyrA p.Asp94Gly (0.94)
Ofloxacin R gyrB p.Arg446Leu (0.15), gyrA p.Asp94Gly (0.94)
Levofloxacin R gyrB p.Arg446Leu (0.15), gyrA p.Asp94Gly (0.94)
Ciprofloxacin R gyrB p.Arg446Leu (0.15), gyrA p.Asp94Gly (0.94)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), ethA c.65delA (1.00), ethA c.65delA (1.00), ethR p.Ala95Thr (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
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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 0.15 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.94 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2288775 c.459_466delCAGGGTGC frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327408 c.65delA frameshift_variant 1.0 ethionamide, ethionamide
ethR 4327831 p.Ala95Thr missense_variant 1.0 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
gyrA 9328 p.Ala676Val missense_variant 0.14
gyrA 9650 c.2349G>A synonymous_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 1.0
rpoC 765618 p.Glu750Gly missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778979 c.-74G>T upstream_gene_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407316 p.Ala9Thr missense_variant 0.11
atpE 1461185 c.141G>A synonymous_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
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155240 p.Ala291Gly missense_variant 0.1
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746350 p.Leu417Met missense_variant 0.12
folC 2746704 p.Ala299Ser missense_variant 0.18
folC 2747731 c.-133C>T upstream_gene_variant 0.13
pepQ 2860189 p.Arg77His missense_variant 0.13
thyX 3067207 p.Ala247Thr missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087504 p.Val229Ile missense_variant 0.12
Rv3083 3449971 c.1470delA frameshift_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612533 p.Ala195Val missense_variant 0.12
Rv3236c 3612557 p.Val187Ala missense_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641990 p.Met152Ile missense_variant 0.17
clpC1 4039540 p.Tyr389Asn missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243159 c.-74C>T upstream_gene_variant 0.12
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244149 p.Trp306* stop_gained 0.12
embB 4248685 c.2172C>G synonymous_variant 0.1
embB 4249054 c.2541C>T synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267679 c.1158G>A synonymous_variant 0.12
aftB 4268140 p.Gly233Arg missense_variant 0.11
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