TB-Profiler result

Run: ERR8665862
Summary

Run ID: ERR8665862

Sample name:

Date: 20-10-2023 16:17:09

Number of reads: 5006053

Percentage reads mapped: 99.69

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.His445Asp (0.58), rpoB p.Ser450Leu (0.41), rpoC p.Ile491Thr (0.32)
Isoniazid R fabG1 c.-15C>T (0.65), fabG1 c.-8T>C (0.37), katG p.Ser315Thr (1.00)
Ethambutol R embA c.-12C>T (0.67), embB p.Met306Ile (0.36), embB p.Gln497Arg (0.48), embB p.Asp1024Asn (0.45)
Pyrazinamide R pncA p.Val139Ala (0.35), pncA p.Asp49Gly (0.70)
Streptomycin R rpsL p.Lys43Arg (0.43), rrs n.514A>C (0.64)
Fluoroquinolones R gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Asp94Gly (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (0.65)
Cycloserine R ald c.464delG (0.37), alr p.Leu113Arg (0.64)
Ethionamide R fabG1 c.-15C>T (0.65), fabG1 c.-8T>C (0.37), ethA c.1386delA (0.33), ethA c.1386delA (0.33)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.34)
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 0.36
lineage4 Euro-American LAM;T;S;X;H None 0.63
lineage4.3 Euro-American (LAM) mainly-LAM None 0.62
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.36
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.35
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.64
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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asp missense_variant 0.58 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.41 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.32 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.43 streptomycin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.64 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.65 isoniazid, ethionamide
fabG1 1673432 c.-8T>C upstream_gene_variant 0.37 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288826 p.Val139Ala missense_variant 0.35 pyrazinamide
pncA 2289096 p.Asp49Gly missense_variant 0.7 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.65 kanamycin
thyX 3067961 c.-16C>T upstream_gene_variant 0.34 para-aminosalicylic_acid
ald 3087278 c.464delG frameshift_variant 0.37 cycloserine
alr 3841083 p.Leu113Arg missense_variant 0.64 cycloserine
embA 4243221 c.-12C>T upstream_gene_variant 0.67 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.36 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.48 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.45 ethambutol
ethA 4326087 c.1386delA frameshift_variant 0.33 ethionamide, 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 0.67
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.36
mshA 575907 p.Ala187Val missense_variant 0.47
ccsA 620625 p.Ile245Met missense_variant 0.32
rpoC 763031 c.-339T>C upstream_gene_variant 0.39
rpoC 764995 c.1626C>G synonymous_variant 0.65
rpoC 766834 p.Glu1155Asp missense_variant 0.72
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.25
mmpL5 776182 p.Asp767Asn missense_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 0.36
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.62
fbiC 1304962 p.Trp678Gly missense_variant 0.79
Rv1258c 1406760 c.580_581insC frameshift_variant 0.31
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.4
rpsA 1834836 p.Met432Thr missense_variant 0.62
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.38
katG 2156196 c.-85C>T upstream_gene_variant 0.67
PPE35 2167926 p.Leu896Ser missense_variant 0.41
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.61
folC 2746340 p.Ala420Val missense_variant 0.75
ribD 2986827 c.-12G>A upstream_gene_variant 0.68
thyA 3073868 p.Thr202Ala missense_variant 0.61
thyA 3073887 c.584delC frameshift_variant 0.38
ald 3086731 c.-89A>G upstream_gene_variant 0.34
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.38
clpC1 4038287 c.2418C>T synonymous_variant 0.61
clpC1 4038968 c.1737G>A synonymous_variant 0.56
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.39
embA 4243460 c.228C>T synonymous_variant 0.38
aftB 4267647 p.Asp397Gly missense_variant 0.3
whiB6 4338371 p.Thr51Pro missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.4
gid 4407927 p.Glu92Asp missense_variant 0.35
gid 4408156 p.Leu16Arg missense_variant 0.71