TB-Profiler result

Run: ERR2510796

Summary

Run ID: ERR2510796

Sample name:

Date: 20-10-2023 06:30:55

Number of reads: 1086484

Percentage reads mapped: 94.36

Strain: lineage4.3.4.2

Drug-resistance: HR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 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
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
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
mmpR5 778996 p.Val3Ile 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 1472106 n.261G>A non_coding_transcript_exon_variant 0.21
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.21
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.21
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.32
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.32
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.24
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.21
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.19
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.25
rrs 1472597 n.752G>A non_coding_transcript_exon_variant 0.2
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.25
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.14
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.25
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.24
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.27
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.28
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.29
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.29
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.3
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.3
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.31
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.28
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.31
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.34
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.25
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.25
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.25
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.24
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.24
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.24
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.24
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.22
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.25
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.22
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.22
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.23
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.35
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.41
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.42
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.39
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.47
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.42
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.31
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519221 c.1107G>A synonymous_variant 1.0
Rv2752c 3065293 p.Val300Ala missense_variant 1.0
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 0.94
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4239763 c.-100C>T upstream_gene_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