TB-Profiler result

Run: ERR9806781
Summary

Run ID: ERR9806781

Sample name:

Date: 18-05-2023 14:48:30

Number of reads: 329986

Percentage reads mapped: 98.75

Strain: lineage4.1.1

Drug-resistance: MDR-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 fabG1 c.-15C>T (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embA c.-16C>G (1.00), embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.Arg154Gly (1.00)
Streptomycin R rrs n.878G>A (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine R ald c.464delG (1.00)
Ethionamide R fabG1 c.-15C>T (1.00), ethA c.1192_1194dupGTG (1.00), ethA c.869dupA (1.00), ethA c.869dupA (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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288782 p.Arg154Gly missense_variant 1.0 pyrazinamide
ald 3087278 c.464delG frameshift_variant 1.0 cycloserine
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326279 c.1192_1194dupGTG conservative_inframe_insertion 1.0 ethionamide
ethA 4326604 c.869dupA 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.89
rpoB 760487 c.681G>A synonymous_variant 0.29
rpoB 762285 p.Arg827Cys missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776350 p.Pro711Thr missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
embR 1416708 p.Ala214Thr missense_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474810 n.1153G>T non_coding_transcript_exon_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168166 p.Thr816Met missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3068080 c.-135C>A upstream_gene_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448892 p.Thr130Ile missense_variant 0.3
Rv3083 3449677 p.Asn392Asp missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613237 c.-121G>T upstream_gene_variant 0.17
fbiB 3642406 p.His291Arg missense_variant 0.29
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4247470 c.957T>C synonymous_variant 0.15
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269853 c.-20C>G upstream_gene_variant 0.2
ethR 4327648 p.Glu34Gln missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0