TB-Profiler result

Run: ERR9806971
Summary

Run ID: ERR9806971

Sample name:

Date: 18-05-2023 20:05:43

Number of reads: 3041372

Percentage reads mapped: 99.54

Strain: lineage4.1.1.3

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), ahpC c.-48G>A (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Val139Met (1.00)
Streptomycin R rpsL p.Lys43Arg (1.00)
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 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
Ethionamide R ethA c.597delC (1.00), ethA c.597delC (1.00)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 1.0
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 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 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155167 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288827 p.Val139Met missense_variant 1.0 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326876 c.597delC frameshift_variant 1.0 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
gyrB 6608 p.Val457Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7857 p.Ala186Thr missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575642 p.Pro99Thr missense_variant 0.11
mshA 575959 c.612G>A synonymous_variant 0.11
mshA 576182 p.Ala279Thr missense_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765570 p.Ala734Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 0.96
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801354 c.546G>A synonymous_variant 1.0
Rv1258c 1406387 c.954C>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472245 n.400C>T non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154828 c.1284G>T synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2859328 p.Arg364Gln missense_variant 0.12
ribD 2987469 c.631C>T synonymous_variant 0.18
ribD 2987512 p.Arg225His missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449616 p.Met371Ile missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embC 4241633 p.Gly591Trp missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244208 c.976C>T synonymous_variant 0.11
embA 4244237 c.1005C>T synonymous_variant 0.11
embA 4245687 p.Val819Phe missense_variant 0.17
embB 4245743 c.-771C>A upstream_gene_variant 0.12
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267883 c.954C>T synonymous_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0