TB-Profiler result

Run: ERR4797787
Summary

Run ID: ERR4797787

Sample name:

Date: 20-10-2023 02:34:48

Number of reads: 4719770

Percentage reads mapped: 99.65

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.Ser450Leu (0.56)
Isoniazid R fabG1 c.-15C>T (0.45), katG p.Ser315Thr (0.39)
Ethambutol R embA c.-11C>A (0.38), embB p.Met306Val (0.38)
Pyrazinamide R pncA p.Leu27Pro (0.38)
Streptomycin R rpsL p.Lys43Arg (0.33)
Fluoroquinolones R gyrA p.Ala90Val (0.40), gyrA p.Asp94Ala (0.30), gyrA p.Asp94Gly (0.69)
Moxifloxacin R gyrA p.Ala90Val (0.40), gyrA p.Asp94Ala (0.30), gyrA p.Asp94Gly (0.69)
Ofloxacin R gyrA p.Ala90Val (0.40), gyrA p.Asp94Ala (0.30), gyrA p.Asp94Gly (0.69)
Levofloxacin R gyrA p.Ala90Val (0.40), gyrA p.Asp94Ala (0.30), gyrA p.Asp94Gly (0.69)
Ciprofloxacin R gyrA p.Ala90Val (0.40), gyrA p.Asp94Ala (0.30), gyrA p.Asp94Gly (0.69)
Aminoglycosides R rrs n.1401A>G (0.41)
Amikacin R rrs n.1401A>G (0.41)
Capreomycin R rrs n.1401A>G (0.41)
Kanamycin R rrs n.1401A>G (0.41)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.45)
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 0.42
lineage4 Euro-American LAM;T;S;X;H None 0.6
lineage4.3 Euro-American (LAM) mainly-LAM None 0.58
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.44
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.44
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.6
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 0.4 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.3 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.69 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.56 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.33 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.41 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.45 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.39 isoniazid
pncA 2289162 p.Leu27Pro missense_variant 0.38 pyrazinamide
embA 4243222 c.-11C>A upstream_gene_variant 0.38 ethambutol
embB 4247429 p.Met306Val missense_variant 0.38 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 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 0.54
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.5
ccsA 620625 p.Ile245Met missense_variant 0.45
rpoC 763031 c.-339T>C upstream_gene_variant 0.53
rpoC 764995 c.1626C>G synonymous_variant 0.51
rpoC 766488 p.Pro1040Arg missense_variant 0.38
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.46
mmpS5 779615 c.-710C>G upstream_gene_variant 0.51
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.44
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.41
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.48
PPE35 2167926 p.Leu896Ser missense_variant 0.42
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.59
thyA 3073868 p.Thr202Ala missense_variant 0.51
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 0.6
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568435 c.242_245delGTCCinsATCCTT frameshift_variant&missense_variant 0.46
whiB7 3568442 p.Lys80Gln missense_variant 0.43
whiB7 3568443 p.His79Gln missense_variant 0.44
whiB7 3568854 c.-176delG upstream_gene_variant 0.4
Rv3236c 3612813 p.Thr102Ala missense_variant 0.45
clpC1 4038287 c.2418C>T synonymous_variant 0.52
embC 4242182 p.Ala774Ser missense_variant 0.47
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.41
aftB 4267647 p.Asp397Gly missense_variant 0.4
ubiA 4268930 p.Gly302Ser missense_variant 0.67
ethA 4326513 p.Thr321Pro missense_variant 0.41
ethA 4326676 p.Ser266Arg missense_variant 0.48
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.44
gid 4407927 p.Glu92Asp missense_variant 0.37
gid 4408156 p.Leu16Arg missense_variant 0.63