TB-Profiler result

Run: ERR9806962
Summary

Run ID: ERR9806962

Sample name:

Date: 18-05-2023 19:54:21

Number of reads: 2387882

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.Trp397* (0.11), 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 0.99
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 2154921 p.Trp397* stop_gained 0.11 isoniazid
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491341 p.Arg187Cys missense_variant 0.12
mshA 575446 c.99A>G synonymous_variant 0.12
mshA 576368 p.Arg341Gly missense_variant 0.14
rpoC 762896 c.-474G>A upstream_gene_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779419 p.Ala144Thr missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801329 p.Arg174Leu missense_variant 0.14
rplC 801354 c.546G>A synonymous_variant 1.0
embR 1417391 c.-44C>A upstream_gene_variant 0.1
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674449 p.Gly83Val missense_variant 0.11
rpsA 1834823 p.His428Asp missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918582 p.Ala215Thr missense_variant 0.11
katG 2155211 p.Lys301Glu missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288804 c.438G>A synonymous_variant 0.16
pncA 2289603 c.-362G>T upstream_gene_variant 0.12
Rv2752c 3067181 c.-990G>T upstream_gene_variant 0.14
thyX 3067652 p.His98Gln missense_variant 0.11
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
fprA 3474229 p.Arg75Ser missense_variant 0.12
alr 3840299 c.1122C>A synonymous_variant 0.12
rpoA 3877949 p.Thr187Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243812 p.Arg194Trp missense_variant 0.13
embA 4245452 c.2220G>C synonymous_variant 0.1
embA 4246170 p.Asp980Asn missense_variant 0.11
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0