TB-Profiler result

Run: ERR11465033
Summary

Run ID: ERR11465033

Sample name:

Date: 07-01-2024 12:50:18

Number of reads: 8352131

Percentage reads mapped: 99.68

Strain: lineage4.8;lineage4.4.1.1

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 (0.52)
Isoniazid R katG p.Ser315Thr (0.28)
Ethambutol R embB p.Met306Val (0.26)
Pyrazinamide R pncA c.158delA (0.28), pncA c.158delA (0.28)
Streptomycin R rrs n.517C>T (0.45)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.3
lineage4.4 Euro-American S;T None 0.7
lineage4.4.1 Euro-American (S-type) S;T None 0.69
lineage4.4.1.1 Euro-American S;Orphans None 0.69
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 0.52 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.45 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.28 isoniazid
pncA 2289083 c.158delA frameshift_variant 0.28 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.26 ethambutol
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 0.6
gyrA 9138 p.Gln613Glu missense_variant 0.62
gyrA 9304 p.Gly668Asp missense_variant 0.68
mshA 576108 p.Ala254Gly missense_variant 0.17
rpoB 762475 p.Gly890Val missense_variant 0.3
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 0.68
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.46
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918420 p.Ala161Thr missense_variant 0.65
ndh 2102990 p.Val18Ala missense_variant 0.77
PPE35 2168149 p.Pro822Ser missense_variant 0.26
PPE35 2168479 p.Thr712Pro missense_variant 0.67
PPE35 2169840 p.Gly258Asp missense_variant 0.82
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715432 c.-100C>T upstream_gene_variant 0.44
folC 2746529 p.Ala357Val missense_variant 0.35
ald 3086788 c.-32T>C upstream_gene_variant 0.65
Rv3083 3448608 c.105G>A synonymous_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.63
whiB7 3568779 c.-100T>C upstream_gene_variant 0.73
Rv3236c 3612665 p.Val151Ala missense_variant 0.73
clpC1 4039729 p.Asp326Asn missense_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.27
embB 4246567 c.54G>T synonymous_variant 0.14
ethA 4326153 p.Arg441Cys missense_variant 0.35
whiB6 4338595 c.-75delG upstream_gene_variant 1.0