TB-Profiler result

Run: ERR8975801

Summary

Run ID: ERR8975801

Sample name:

Date: 20-10-2023 15:45:32

Number of reads: 6810179

Percentage reads mapped: 99.7

Strain: lineage4.3.3;lineage2.2.1.1

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.Ile491Phe (0.30)
Isoniazid R fabG1 c.-8T>A (0.24), katG p.Ser315Thr (0.25)
Ethambutol R embB p.Met306Val (0.26)
Pyrazinamide R pncA p.Gly132Ala (0.29)
Streptomycin
Fluoroquinolones R gyrA p.Asp94Gly (0.28)
Moxifloxacin R gyrA p.Asp94Gly (0.28)
Ofloxacin R gyrA p.Asp94Gly (0.28)
Levofloxacin R gyrA p.Asp94Gly (0.28)
Ciprofloxacin R gyrA p.Asp94Gly (0.28)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.-11A>G (0.32)
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 0.73
lineage4 Euro-American LAM;T;S;X;H None 0.27
lineage4.3 Euro-American (LAM) mainly-LAM None 0.27
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.72
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.73
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.29
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.72
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 7582 p.Asp94Gly missense_variant 0.28 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761277 p.Ile491Phe missense_variant 0.3 rifampicin
fabG1 1673432 c.-8T>A upstream_gene_variant 0.24 isoniazid
katG 2155168 p.Ser315Thr missense_variant 0.25 isoniazid
pncA 2288847 p.Gly132Ala missense_variant 0.29 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.26 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 0.32 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 8040 p.Gly247Ser missense_variant 0.23
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.69
mshA 575907 p.Ala187Val missense_variant 0.76
ccsA 620625 p.Ile245Met missense_variant 0.7
rpoB 761283 p.Ser493Thr missense_variant 0.31
rpoC 763031 c.-339T>C upstream_gene_variant 0.73
rpoC 764995 c.1626C>G synonymous_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.71
mmpL5 776182 p.Asp767Asn missense_variant 0.72
mmpS5 779615 c.-710C>G upstream_gene_variant 0.74
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.75
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.29
rpsA 1834177 c.636A>C synonymous_variant 0.7
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.73
PPE35 2167926 p.Leu896Ser missense_variant 0.75
Rv1979c 2223014 p.Tyr51Asn missense_variant 0.7
Rv1979c 2223051 p.Glu38Asp missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.31
eis 2714846 p.Val163Ile missense_variant 0.77
Rv2752c 3065824 p.Pro123Leu missense_variant 0.27
thyA 3073868 p.Thr202Ala missense_variant 0.26
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612471 p.Glu216Lys missense_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 0.67
clpC1 4038287 c.2418C>T synonymous_variant 0.31
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.78
embB 4248115 c.1602C>T synonymous_variant 0.72
aftB 4267647 p.Asp397Gly missense_variant 0.73
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.69
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.18