TB-Profiler result

Run: ERR7911636
Summary

Run ID: ERR7911636

Sample name:

Date: 19-10-2023 13:31:07

Number of reads: 4339826

Percentage reads mapped: 99.52

Strain: lineage4.1.1.3;lineage2.2.2

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 (0.46), rpoB p.Ser450Leu (0.59)
Isoniazid R fabG1 c.-17G>T (0.46), katG p.Ser315Thr (0.61), ahpC c.-48G>A (0.62)
Ethambutol R embB p.Met306Val (0.59)
Pyrazinamide R pncA c.517dupG (0.49), pncA c.517dupG (0.49), pncA p.Val139Met (0.48)
Streptomycin R rpsL p.Lys43Arg (0.50), rrs n.514A>C (0.44), gid p.Leu79Ser (0.48)
Fluoroquinolones R gyrA p.Ala90Val (0.52), gyrA p.Asp94Gly (0.48)
Moxifloxacin R gyrA p.Ala90Val (0.52), gyrA p.Asp94Gly (0.48)
Ofloxacin R gyrA p.Ala90Val (0.52), gyrA p.Asp94Gly (0.48)
Levofloxacin R gyrA p.Ala90Val (0.52), gyrA p.Asp94Gly (0.48)
Ciprofloxacin R gyrA p.Ala90Val (0.52), gyrA p.Asp94Gly (0.48)
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
Cycloserine R alr p.Leu113Arg (0.47)
Ethionamide R fabG1 c.-17G>T (0.46), ethA p.Ala381Pro (0.48), ethA c.597delC (0.56), ethA c.597delC (0.56)
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 0.47
lineage4 Euro-American LAM;T;S;X;H None 0.54
lineage4.1 Euro-American T;X;H None 0.56
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.47
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.42
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.56
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.55
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 0.52 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.48 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.46 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.59 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.5 streptomycin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.44 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673423 c.-17G>T upstream_gene_variant 0.46 isoniazid, ethionamide
katG 2155167 p.Ser315Thr missense_variant 0.61 isoniazid
pncA 2288724 c.517dupG frameshift_variant 0.49 pyrazinamide, pyrazinamide
pncA 2288827 p.Val139Met missense_variant 0.48 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 0.62 isoniazid
alr 3841083 p.Leu113Arg missense_variant 0.47 cycloserine
embB 4247429 p.Met306Val missense_variant 0.59 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 0.48 ethionamide
ethA 4326876 c.597delC frameshift_variant 0.56 ethionamide, ethionamide
gid 4407967 p.Leu79Ser missense_variant 0.48 streptomycin
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
gyrB 6608 p.Val457Leu missense_variant 0.54
gyrA 7362 p.Glu21Gln missense_variant 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.43
rpoC 763031 c.-339T>C upstream_gene_variant 0.55
rpoC 765150 p.Gly594Glu missense_variant 0.44
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.43
mmpS5 779615 c.-710C>G upstream_gene_variant 0.39
rpsL 781395 c.-165T>C upstream_gene_variant 0.6
rplC 801354 c.546G>A synonymous_variant 0.58
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 0.37
PPE35 2167926 p.Leu896Ser missense_variant 0.42
Rv1979c 2221939 p.Arg409Gln missense_variant 0.48
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449616 p.Met371Ile missense_variant 0.6
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.41
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.61
embA 4243460 c.228C>T synonymous_variant 0.46
embB 4249408 c.2895G>A synonymous_variant 0.56
aftB 4267647 p.Asp397Gly missense_variant 0.37
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.49
gid 4407927 p.Glu92Asp missense_variant 0.43