TB-Profiler result

Run: ERR1035312
Summary

Run ID: ERR1035312

Sample name:

Date: 20-10-2023 21:38:58

Number of reads: 5848725

Percentage reads mapped: 98.7

Strain: lineage4.3.3

Drug-resistance: Pre-XDR-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.Ser450Trp (1.00)
Isoniazid
Ethambutol R embA c.-12C>T (1.00)
Pyrazinamide R pncA p.Trp68Arg (1.00)
Streptomycin
Fluoroquinolones R gyrA p.Ala90Val (1.00)
Moxifloxacin R gyrA p.Ala90Val (1.00)
Ofloxacin R gyrA p.Ala90Val (1.00)
Levofloxacin R gyrA p.Ala90Val (1.00)
Ciprofloxacin R gyrA p.Ala90Val (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine R ald c.436_437dupGC (0.96)
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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Trp missense_variant 1.0 rifampicin
pncA 2289040 p.Trp68Arg missense_variant 1.0 pyrazinamide
ald 3087252 c.436_437dupGC frameshift_variant 0.96 cycloserine
embA 4243221 c.-12C>T upstream_gene_variant 1.0 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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764582 c.1213C>T synonymous_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765804 p.Thr812Ile missense_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
rrs 1471969 n.124T>C non_coding_transcript_exon_variant 0.47
rrl 1473752 n.95G>T non_coding_transcript_exon_variant 0.46
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.53
rrl 1473815 n.158T>C non_coding_transcript_exon_variant 0.59
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.61
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.34
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.34
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.39
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.32
rrl 1473944 n.287G>T non_coding_transcript_exon_variant 0.32
rrl 1473981 n.324delGinsAT non_coding_transcript_exon_variant 0.21
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.3
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.36
rrl 1474028 n.371T>C non_coding_transcript_exon_variant 0.34
rrl 1474029 n.372G>A non_coding_transcript_exon_variant 0.34
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.36
rrl 1474040 n.383G>A non_coding_transcript_exon_variant 0.42
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.29
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.31
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.33
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.38
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.41
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.21
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.28
rrl 1474716 n.1059A>G non_coding_transcript_exon_variant 0.31
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.29
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.29
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.29
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.36
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.31
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.31
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.38
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.38
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.28
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.27
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.28
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.19
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.37
rrl 1476629 n.2972C>A non_coding_transcript_exon_variant 0.37
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.21
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.19
rpsA 1833678 p.Val46Ala missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.97
kasA 2518919 p.Gly269Ser missense_variant 1.0
Rv2752c 3066014 c.177dupG frameshift_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.97
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245187 p.Thr652Lys missense_variant 1.0
ubiA 4268987 p.Val283Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408105 p.Arg33Pro missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0