TB-Profiler result

Run: ERR11243572
Summary

Run ID: ERR11243572

Sample name:

Date: 21-04-2023 23:31:33

Number of reads: 5885384

Percentage reads mapped: 99.71

Strain: lineage4.8

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 (0.99)
Isoniazid R fabG1 c.-15C>T (1.00)
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 761155 p.Ser450Leu missense_variant 0.99 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, 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
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407062 c.279G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474425 n.768A>G non_coding_transcript_exon_variant 0.25
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.24
rpsA 1833641 p.Asn34Asp missense_variant 0.11
rpsA 1833651 p.Asp37Ala missense_variant 0.12
rpsA 1833658 c.117C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.11
PPE35 2170053 p.Thr187Ser missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518348 c.234A>T synonymous_variant 0.13
folC 2747750 c.-152G>A upstream_gene_variant 1.0
fbiD 3339741 c.624G>T synonymous_variant 0.12
fbiD 3339744 c.627A>C synonymous_variant 0.12
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
rpoA 3878567 c.-60C>G upstream_gene_variant 0.12
rpoA 3878599 c.-92C>G upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243331 c.99G>T synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.32
embB 4246548 p.Pro12Gln missense_variant 0.34
embB 4246555 c.42G>C synonymous_variant 0.36
embB 4246556 p.Ala15Pro missense_variant 0.36
embB 4246563 p.Leu17Trp missense_variant 0.37
embB 4246567 c.54G>T synonymous_variant 0.39
aftB 4268078 c.759C>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408059 p.His48Gln missense_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0