TB-Profiler result

Run: ERR1213873

Summary

Run ID: ERR1213873

Sample name:

Date: 19-10-2023 20:51:06

Number of reads: 4803370

Percentage reads mapped: 97.91

Strain: lineage4.3.4.2.1

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.Asp435Val (1.00)
Isoniazid R katG p.Ser315Thr (0.95)
Ethambutol
Pyrazinamide
Streptomycin R rrs n.462C>T (0.33)
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 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 0.99
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.99
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.33 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.95 isoniazid
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
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416911 p.Arg146His missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472300 n.455C>T non_coding_transcript_exon_variant 0.33
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.42
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.59
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.56
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.6
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.49
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.49
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.44
rrl 1473923 n.266C>A non_coding_transcript_exon_variant 0.53
rrl 1473924 n.267_268insT non_coding_transcript_exon_variant 0.53
rrl 1473981 n.324delGinsAT non_coding_transcript_exon_variant 0.45
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.42
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.43
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.38
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.36
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.44
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.49
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.52
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.55
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.72
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.74
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.7
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.48
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.46
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.38
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.39
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.5
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.48
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.5
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.23
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.19
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.19
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.39
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.36
rrl 1475289 n.1632G>A non_coding_transcript_exon_variant 0.38
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.38
rrl 1475297 n.1640C>T non_coding_transcript_exon_variant 0.5
rrl 1475315 n.1658A>C non_coding_transcript_exon_variant 0.59
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.47
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.5
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.42
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.4
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.4
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.35
rrl 1475446 n.1789G>C non_coding_transcript_exon_variant 0.31
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.3
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.28
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.21
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.21
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.34
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.34
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 0.97
Rv1979c 2222417 p.Arg250Trp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.98
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 0.96
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
aftB 4269056 c.-220C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407724 p.Leu160Pro missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0