TB-Profiler result

Run: ERR4800302
Summary

Run ID: ERR4800302

Sample name:

Date: 20-10-2023 04:15:18

Number of reads: 2644315

Percentage reads mapped: 99.57

Strain: lineage4.4.1.1;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 (0.25)
Isoniazid R katG p.Ser315Thr (0.15)
Ethambutol R embB p.Gln497Arg (0.34)
Pyrazinamide R pncA c.149delT (0.34)
Streptomycin R gid c.351delG (0.27)
Fluoroquinolones R gyrA p.Ala90Val (0.19)
Moxifloxacin R gyrA p.Ala90Val (0.19)
Ofloxacin R gyrA p.Ala90Val (0.19)
Levofloxacin R gyrA p.Ala90Val (0.19)
Ciprofloxacin R gyrA p.Ala90Val (0.19)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
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 0.77
lineage4 Euro-American LAM;T;S;X;H None 0.25
lineage4.4 Euro-American S;T None 0.26
lineage4.4.1 Euro-American (S-type) S;T None 0.27
lineage4.4.1.1 Euro-American S;Orphans None 0.23
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 0.19 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.25 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.15 isoniazid
pncA 2289092 c.149delT frameshift_variant 0.34 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.34 ethambutol
gid 4407851 c.351delG frameshift_variant 0.27 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
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 491742 c.960T>C synonymous_variant 0.83
rpoB 759746 c.-61C>T upstream_gene_variant 0.62
rpoC 762434 c.-936T>G upstream_gene_variant 0.77
rpoC 763031 c.-339T>C upstream_gene_variant 0.81
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.81
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 0.75
PPE35 2167926 p.Leu896Ser missense_variant 0.72
PPE35 2169840 p.Gly258Asp missense_variant 0.28
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.71
pncA 2289365 c.-125delC upstream_gene_variant 0.69
ahpC 2726105 c.-88G>A upstream_gene_variant 0.77
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.28
Rv3083 3448684 p.Thr61Ala missense_variant 0.73
Rv3083 3449922 c.1419G>A synonymous_variant 0.68
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 0.2
ddn 3986977 p.Pro45Leu missense_variant 0.23
clpC1 4039667 p.Gln346His missense_variant 0.73
clpC1 4040126 c.579C>T synonymous_variant 0.63
embC 4242075 p.Arg738Gln missense_variant 0.72
embA 4242643 c.-590C>T upstream_gene_variant 0.98
embA 4243129 c.-104G>A upstream_gene_variant 0.3
embA 4244050 p.Asp273Gly missense_variant 0.73
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.76