TB-Profiler result

Run: ERR2513819

Summary

Run ID: ERR2513819

Sample name:

Date: 20-10-2023 11:15:26

Number of reads: 1981723

Percentage reads mapped: 94.61

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.His445Asp (1.00)
Isoniazid R fabG1 c.-15C>T (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embA c.-12C>T (1.00), embB p.Gln497Arg (1.00)
Pyrazinamide R pncA c.-5delG (1.00)
Streptomycin R rrs n.514A>C (1.00)
Fluoroquinolones R gyrA p.Gly88Cys (1.00)
Moxifloxacin R gyrA p.Gly88Cys (1.00)
Ofloxacin R gyrA p.Gly88Cys (1.00)
Levofloxacin R gyrA p.Gly88Cys (1.00)
Ciprofloxacin R gyrA p.Gly88Cys (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine R alr p.Leu113Arg (1.00)
Ethionamide R fabG1 c.-15C>T (1.00), ethA c.699_700dupGG (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
lineage4.3 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 7563 p.Gly88Cys missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289245 c.-5delG upstream_gene_variant 1.0 pyrazinamide
alr 3841083 p.Leu113Arg missense_variant 1.0 cycloserine
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4326773 c.699_700dupGG frameshift_variant 1.0 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
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 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
fbiC 1303095 c.165G>A synonymous_variant 1.0
fbiC 1304962 p.Trp678Gly missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>G non_coding_transcript_exon_variant 0.33
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.33
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.43
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.43
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.45
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.54
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.57
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.64
rrs 1473081 n.1236C>T non_coding_transcript_exon_variant 0.48
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.66
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.64
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.64
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.46
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.66
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.66
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.69
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.4
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.73
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.61
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.71
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.63
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.63
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.63
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.57
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.48
rrl 1474636 n.979A>C non_coding_transcript_exon_variant 0.63
rrl 1474637 n.980C>G non_coding_transcript_exon_variant 0.61
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.61
rrl 1474643 n.986A>G non_coding_transcript_exon_variant 0.61
rrl 1474663 n.1006C>T non_coding_transcript_exon_variant 0.68
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.61
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.6
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.6
rrl 1474692 n.1035G>A non_coding_transcript_exon_variant 0.61
rrl 1474706 n.1049G>A non_coding_transcript_exon_variant 0.4
rrl 1474711 n.1054_1056delGGTinsCCGG non_coding_transcript_exon_variant 0.44
rrl 1474717 n.1060A>T non_coding_transcript_exon_variant 0.44
rrl 1474734 n.1077G>A non_coding_transcript_exon_variant 0.39
rrl 1474736 n.1079C>T non_coding_transcript_exon_variant 0.37
rrl 1474753 n.1096_1097delACinsT non_coding_transcript_exon_variant 0.35
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.39
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.39
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746340 p.Ala420Val missense_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 0.97
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
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0