TB-Profiler result

Run: ERR4821318

Summary

Run ID: ERR4821318

Sample name:

Date: 20-10-2023 09:36:27

Number of reads: 3408955

Percentage reads mapped: 93.86

Strain: lineage4.6.2.2

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 R rrs n.1402C>A (0.44)
Amikacin R rrs n.1402C>A (0.44)
Capreomycin R rrs n.1402C>A (0.44)
Kanamycin R rrs n.1402C>A (0.44)
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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.2 Euro-American T;LAM RD726 1.0
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 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
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.44 kanamycin, capreomycin, aminoglycosides, amikacin
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
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778298 c.-692C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472148 n.303T>C non_coding_transcript_exon_variant 0.56
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.56
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.62
rrs 1472188 n.343A>G non_coding_transcript_exon_variant 0.76
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.79
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.73
rrs 1472251 n.406G>C non_coding_transcript_exon_variant 0.85
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.6
rrs 1472623 n.778A>C non_coding_transcript_exon_variant 0.57
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.72
rrs 1472674 n.829T>C non_coding_transcript_exon_variant 0.82
rrs 1472675 n.830T>G non_coding_transcript_exon_variant 0.82
rrs 1472677 n.832C>A non_coding_transcript_exon_variant 0.82
rrs 1472682 n.837T>A non_coding_transcript_exon_variant 0.82
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.82
rrs 1472685 n.840G>T non_coding_transcript_exon_variant 0.82
rrs 1472701 n.856T>C non_coding_transcript_exon_variant 0.87
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.75
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.74
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.67
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.57
rrs 1472957 n.1112C>A non_coding_transcript_exon_variant 0.57
rrs 1472969 n.1125delC non_coding_transcript_exon_variant 0.57
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.57
rrs 1472974 n.1129A>C non_coding_transcript_exon_variant 0.57
rrs 1472975 n.1130T>G non_coding_transcript_exon_variant 0.57
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.6
rrs 1472989 n.1144G>T non_coding_transcript_exon_variant 0.65
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.65
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.81
rrs 1473029 n.1184C>G non_coding_transcript_exon_variant 0.67
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.37
rrs 1473226 n.1381C>G non_coding_transcript_exon_variant 0.48
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.31
rrs 1473284 n.1439A>G non_coding_transcript_exon_variant 0.23
rrs 1473285 n.1440A>T non_coding_transcript_exon_variant 0.23
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.2
rrs 1473292 n.1447_1449delGGAinsTGGG non_coding_transcript_exon_variant 0.21
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.24
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.46
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.6
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.61
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.71
rrl 1475978 n.2321C>T non_coding_transcript_exon_variant 0.71
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.67
rrl 1475991 n.2334T>A non_coding_transcript_exon_variant 0.67
rrl 1475997 n.2340A>G non_coding_transcript_exon_variant 0.71
rrl 1476001 n.2344T>C non_coding_transcript_exon_variant 0.67
rrl 1476187 n.2530T>C non_coding_transcript_exon_variant 0.78
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.81
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.85
rrl 1476207 n.2550T>C non_coding_transcript_exon_variant 0.85
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.83
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.8
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.77
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.62
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.67
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.92
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.92
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.85
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.79
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.79
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.79
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.79
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.82
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.67
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155389 c.723C>G synonymous_variant 1.0
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067474 p.Pro158Ala missense_variant 1.0
Rv3083 3448567 p.His22Asp missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612571 c.546C>T synonymous_variant 0.99
Rv3236c 3612910 p.Leu69Phe missense_variant 1.0
embA 4242550 c.-683C>G upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245700 p.Gly823Glu missense_variant 1.0
aftB 4267272 p.Lys522Arg missense_variant 1.0
ethR 4326739 c.-810G>C upstream_gene_variant 1.0
ethA 4328004 c.-531C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0