TB-Profiler result

Run: SRR6824678
Summary

Run ID: SRR6824678

Sample name:

Date: 20-10-2023 19:33:11

Number of reads: 9600184

Percentage reads mapped: 99.04

Strain: lineage4.2.2

Drug-resistance: RR-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.Thr400Ala (1.00), rpoB p.Ser450Leu (0.99)
Isoniazid
Ethambutol R embB p.Met306Ile (0.99)
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
lineage4.2 Euro-American H;T;LAM None 0.99
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
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 761004 p.Thr400Ala missense_variant 1.0 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
embB 4247431 p.Met306Ile missense_variant 0.99 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 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406372 c.969G>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.12
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.11
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.11
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.12
rrs 1473097 n.1252G>A non_coding_transcript_exon_variant 0.18
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.18
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.17
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.17
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.17
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.17
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.17
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.17
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15
rrs 1473147 n.1302G>A non_coding_transcript_exon_variant 0.15
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.14
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.14
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.17
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.16
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.16
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.16
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.17
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.17
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154980 p.Leu378Met missense_variant 1.0
katG 2155819 p.Tyr98Cys missense_variant 1.0
PPE35 2168121 p.Leu831His missense_variant 1.0
PPE35 2168805 p.Gly603Asp missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339145 p.Ile10Val missense_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612469 c.648A>G synonymous_variant 0.99
alr 3841567 c.-147A>G upstream_gene_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338593 c.-73delT upstream_gene_variant 1.0
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0