TB-Profiler result

Run: ERR4798816
Summary

Run ID: ERR4798816

Sample name:

Date: 20-10-2023 03:11:21

Number of reads: 4303002

Percentage reads mapped: 99.65

Strain: lineage4.9;lineage4.1.1.3;lineage3;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 (0.45)
Isoniazid R fabG1 c.-15C>T (0.44), katG p.Ser315Thr (0.52)
Ethambutol R embA c.-16C>T (0.38), embB p.Gly406Ser (0.44)
Pyrazinamide R pncA c.391dupG (0.46), pncA c.391dupG (0.46)
Streptomycin R rpsL p.Lys43Arg (0.40)
Fluoroquinolones R gyrA p.Ala90Val (0.43), gyrA p.Asp94Gly (0.46)
Moxifloxacin R gyrA p.Ala90Val (0.43), gyrA p.Asp94Gly (0.46)
Ofloxacin R gyrA p.Ala90Val (0.43), gyrA p.Asp94Gly (0.46)
Levofloxacin R gyrA p.Ala90Val (0.43), gyrA p.Asp94Gly (0.46)
Ciprofloxacin R gyrA p.Ala90Val (0.43), gyrA p.Asp94Gly (0.46)
Aminoglycosides R rrs n.1401A>G (0.30)
Amikacin R rrs n.1401A>G (0.30)
Capreomycin R rrs n.1401A>G (0.30)
Kanamycin R rrs n.1401A>G (0.30)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.44)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.22
lineage2 East-Asian Beijing RD105 0.45
lineage4 Euro-American LAM;T;S;X;H None 0.34
lineage4.1 Euro-American T;X;H None 0.09
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.43
lineage4.9 Euro-American (H37Rv-like) T1 None 0.2
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.46
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.11
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.11
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 7570 p.Ala90Val missense_variant 0.43 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.46 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.45 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.4 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.3 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.44 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.52 isoniazid
pncA 2288850 c.391dupG frameshift_variant 0.46 pyrazinamide, pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.38 ethambutol
embB 4247729 p.Gly406Ser missense_variant 0.44 ethambutol
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 0.85
gyrA 9304 p.Gly668Asp missense_variant 0.79
fgd1 491742 c.960T>C synonymous_variant 0.78
mshA 575907 p.Ala187Val missense_variant 0.55
ccsA 620625 p.Ile245Met missense_variant 0.46
rpoB 759746 c.-61C>T upstream_gene_variant 0.24
rpoC 762434 c.-936T>G upstream_gene_variant 0.19
rpoC 763031 c.-339T>C upstream_gene_variant 0.65
rpoC 764723 p.Phe452Leu missense_variant 0.44
mmpL5 775639 p.Ile948Val missense_variant 0.77
mmpL5 776100 p.Thr794Ile missense_variant 0.79
mmpL5 776182 p.Asp767Asn missense_variant 0.47
mmpS5 779615 c.-710C>G upstream_gene_variant 0.38
rpsL 781395 c.-165T>C upstream_gene_variant 0.85
fbiC 1303326 c.396C>T synonymous_variant 0.38
Rv1258c 1406760 c.580_581insC frameshift_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.43
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.68
PPE35 2167926 p.Leu896Ser missense_variant 0.77
PPE35 2168686 p.Thr643Ala missense_variant 0.12
Rv1979c 2222357 p.Thr270Ala missense_variant 0.48
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.9
pncA 2289047 c.195C>T synonymous_variant 0.25
pncA 2289365 c.-125delC upstream_gene_variant 0.29
ahpC 2726105 c.-88G>A upstream_gene_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 0.85
fprA 3473810 c.-197A>G upstream_gene_variant 0.49
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.75
Rv3236c 3612813 p.Thr102Ala missense_variant 0.47
alr 3841473 c.-53G>A upstream_gene_variant 0.26
clpC1 4039799 c.906C>T synonymous_variant 0.17
embC 4242075 p.Arg738Gln missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 0.81
embC 4242803 p.Val981Leu missense_variant 0.11
embA 4243460 c.228C>T synonymous_variant 0.35
aftB 4267647 p.Asp397Gly missense_variant 0.48
whiB6 4338333 c.188dupC frameshift_variant 0.45
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.66
gid 4407927 p.Glu92Asp missense_variant 0.47