TB-Profiler result

Run: ERR1035046
Summary

Run ID: ERR1035046

Sample name:

Date: 20-10-2023 23:35:02

Number of reads: 7620364

Percentage reads mapped: 99.46

Strain: lineage4.7;lineage3

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 (0.45)
Isoniazid R inhA c.-154G>A (0.45), katG p.Ser315Thr (0.48)
Ethambutol R embB p.Met306Ile (0.57)
Pyrazinamide R pncA p.Gly97Asp (0.43)
Streptomycin
Fluoroquinolones R gyrA p.Ala90Val (0.45)
Moxifloxacin R gyrA p.Ala90Val (0.45)
Ofloxacin R gyrA p.Ala90Val (0.45)
Levofloxacin R gyrA p.Ala90Val (0.45)
Ciprofloxacin R gyrA p.Ala90Val (0.45)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R inhA c.-154G>A (0.45), ethA p.Thr342Lys (0.49)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage3 East-African-Indian CAS RD750 0.55
lineage4 Euro-American LAM;T;S;X;H None 0.45
lineage4.7 Euro-American (mainly T) T1;T5 None 0.45
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 0.45 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.45 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 0.45 isoniazid, ethionamide
katG 2155167 p.Ser315Thr missense_variant 0.48 isoniazid
pncA 2288952 p.Gly97Asp missense_variant 0.43 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.57 ethambutol
ethA 4326449 p.Thr342Lys missense_variant 0.49 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 0.56
gyrA 8056 p.Arg252Leu missense_variant 0.58
gyrA 9304 p.Gly668Asp missense_variant 0.56
fgd1 491742 c.960T>C synonymous_variant 0.52
rpoB 759746 c.-61C>T upstream_gene_variant 0.52
rpoC 762434 c.-936T>G upstream_gene_variant 0.56
rpoC 763031 c.-339T>C upstream_gene_variant 0.51
rpoC 764817 p.Val483Gly missense_variant 0.38
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.49
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 0.45
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.57
PPE35 2167926 p.Leu896Ser missense_variant 0.57
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.57
pncA 2289365 c.-125delC upstream_gene_variant 0.58
ahpC 2726105 c.-88G>A upstream_gene_variant 0.6
thyA 3074424 c.48G>T synonymous_variant 0.58
ald 3086788 c.-32T>C upstream_gene_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.58
embC 4242075 p.Arg738Gln missense_variant 0.47
embA 4242643 c.-590C>T upstream_gene_variant 0.98
embB 4249732 c.3219C>G synonymous_variant 0.43
ethA 4328212 c.-740delC upstream_gene_variant 0.5
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.58
gid 4407704 p.Ala167Pro missense_variant 0.42