TB-Profiler result

Run: ERR11465360
Summary

Run ID: ERR11465360

Sample name:

Date: 09-01-2024 21:55:15

Number of reads: 926853

Percentage reads mapped: 99.2

Strain: lineage4.3.4.1

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.His445Ser (0.89), rpoB p.Ala451Val (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Gln497Arg (0.97)
Pyrazinamide
Streptomycin
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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.96
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 1.0
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 761139 p.His445Ser missense_variant 0.89 rifampicin
rpoB 761158 p.Ala451Val missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4248003 p.Gln497Arg missense_variant 0.97 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 1.0
gyrA 8126 c.825G>C synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766672 c.3303T>C synonymous_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.14
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.19
rrl 1474716 n.1059A>C non_coding_transcript_exon_variant 0.18
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.21
rrl 1475443 n.1786G>A non_coding_transcript_exon_variant 0.21
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.17
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.14
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.13
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.13
rrl 1476580 n.2923G>A non_coding_transcript_exon_variant 0.24
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.25
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.22
rpsA 1833958 p.Ile139Met missense_variant 0.94
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222854 p.Ile104Thr missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064523 p.Glu557Lys missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiA 3640381 c.-162T>C upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039991 c.714G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326129 p.Gln449* stop_gained 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0