TB-Profiler result

Run: ERR4813187
Summary

Run ID: ERR4813187

Sample name:

Date: 20-10-2023 05:08:31

Number of reads: 3530601

Percentage reads mapped: 99.64

Strain: lineage4.3.3;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.Asp435Val (0.74)
Isoniazid R katG p.Ser315Thr (0.71)
Ethambutol R embB p.Met306Val (0.67)
Pyrazinamide R pncA p.Lys48Thr (0.71)
Streptomycin
Fluoroquinolones R gyrA p.Asp94Gly (0.72)
Moxifloxacin R gyrA p.Asp94Gly (0.72)
Ofloxacin R gyrA p.Asp94Gly (0.72)
Levofloxacin R gyrA p.Asp94Gly (0.72)
Ciprofloxacin R gyrA p.Asp94Gly (0.72)
Aminoglycosides R rrs n.1401A>G (0.60)
Amikacin R rrs n.1401A>G (0.60)
Capreomycin R rrs n.1401A>G (0.60)
Kanamycin R rrs n.1401A>G (0.60)
Cycloserine
Ethionamide R ethA p.Pro378Leu (0.72)
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 0.33
lineage4 Euro-American LAM;T;S;X;H None 0.74
lineage4.3 Euro-American (LAM) mainly-LAM None 0.7
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.28
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.28
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.7
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 0.72 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.74 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.6 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.71 isoniazid
pncA 2289099 p.Lys48Thr missense_variant 0.71 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.67 ethambutol
ethA 4326341 p.Pro378Leu missense_variant 0.72 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 0.72
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.31
mshA 575907 p.Ala187Val missense_variant 0.33
ccsA 620625 p.Ile245Met missense_variant 0.4
rpoC 763031 c.-339T>C upstream_gene_variant 0.29
rpoC 764995 c.1626C>G synonymous_variant 0.66
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.23
mmpL5 776182 p.Asp767Asn missense_variant 0.28
mmpS5 779615 c.-710C>G upstream_gene_variant 0.36
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303897 c.967C>T synonymous_variant 0.24
Rv1258c 1406760 c.580_581insC frameshift_variant 0.26
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.73
thyA 3073868 p.Thr202Ala missense_variant 0.73
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087668 c.850dupG frameshift_variant 0.67
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.3
fbiB 3642651 p.Phe373Ile missense_variant 0.31
clpC1 4038287 c.2418C>T synonymous_variant 0.58
embC 4242182 p.Ala774Ser missense_variant 0.72
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243392 p.Asn54Asp missense_variant 0.71
embA 4243460 c.228C>T synonymous_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 0.29
ubiA 4269731 p.Ala35Ser missense_variant 0.73
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.29
gid 4407927 p.Glu92Asp missense_variant 0.3
gid 4407986 p.Gly73Arg missense_variant 0.72
gid 4408156 p.Leu16Arg missense_variant 0.76
gid 4408413 c.-211C>T upstream_gene_variant 0.27