TB-Profiler result

Run: ERR4797192
Summary

Run ID: ERR4797192

Sample name:

Date: 20-10-2023 02:13:02

Number of reads: 6196480

Percentage reads mapped: 99.7

Strain: lineage4.3.4.2;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 katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.31), embB p.Asp1024Asn (0.52)
Pyrazinamide R pncA p.Ala134Val (0.65)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrA p.Asp94Gly (0.92)
Moxifloxacin R gyrA p.Asp94Gly (0.92)
Ofloxacin R gyrA p.Asp94Gly (0.92)
Levofloxacin R gyrA p.Asp94Gly (0.92)
Ciprofloxacin R gyrA p.Asp94Gly (0.92)
Aminoglycosides R rrs n.1401A>G (0.69)
Amikacin R rrs n.1401A>G (0.69)
Capreomycin R rrs n.1401A>G (0.69)
Kanamycin R rrs n.1401A>G (0.69)
Cycloserine
Ethionamide R ethA c.756dupC (0.57)
Clofazimine
Para-aminosalicylic_acid R folC p.Arg49Trp (0.66)
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 0.38
lineage4 Euro-American LAM;T;S;X;H None 0.67
lineage4.3 Euro-American (LAM) mainly-LAM None 0.61
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.36
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.34
lineage4.3.4 Euro-American (LAM) LAM RD174 0.65
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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 0.92 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.69 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288841 p.Ala134Val missense_variant 0.65 pyrazinamide
folC 2747454 p.Arg49Trp missense_variant 0.66 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.31 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.52 ethambutol
ethA 4326717 c.756dupC frameshift_variant 0.57 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
fgd1 491742 c.960T>C synonymous_variant 0.37
mshA 575907 p.Ala187Val missense_variant 0.39
ccsA 620553 c.663T>C synonymous_variant 0.27
ccsA 620625 p.Ile245Met missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 0.47
rpoC 764817 p.Val483Ala missense_variant 0.33
rpoC 764840 p.Ile491Val missense_variant 0.64
rpoC 764995 c.1626C>G synonymous_variant 0.65
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 0.36
mmpL5 776182 p.Asp767Asn missense_variant 0.38
mmpS5 779615 c.-710C>G upstream_gene_variant 0.39
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.35
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.42
PPE35 2167926 p.Leu896Ser missense_variant 0.45
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065293 p.Val300Ala missense_variant 0.68
thyA 3073868 p.Thr202Ala missense_variant 0.65
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 0.65
Rv3236c 3612813 p.Thr102Ala missense_variant 0.35
fbiB 3642600 p.Gly356Arg missense_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 0.71
embC 4239763 c.-100C>T upstream_gene_variant 0.66
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.35
embB 4249757 p.Thr1082Ala missense_variant 0.4
aftB 4267647 p.Asp397Gly missense_variant 0.31
whiB6 4338595 c.-75delG upstream_gene_variant 0.35
gid 4407588 c.615A>G synonymous_variant 0.41
gid 4407927 p.Glu92Asp missense_variant 0.34
gid 4408156 p.Leu16Arg missense_variant 0.63