TB-Profiler result

Run: ERR4828843

Summary

Run ID: ERR4828843

Sample name:

Date: 20-10-2023 15:24:04

Number of reads: 4146027

Percentage reads mapped: 96.41

Strain: lineage4.2.2.2

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.Ser450Leu (0.99)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Gly406Ala (0.99)
Pyrazinamide R pncA p.Thr76Pro (1.00)
Streptomycin R rpsL p.Lys88Thr (1.00), rrs n.888G>A (0.18), gid p.Gly69Asp (1.00)
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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 1.0
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 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
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rpsL 781822 p.Lys88Thr missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.18 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.99 ethambutol
gid 4407997 p.Gly69Asp missense_variant 1.0 streptomycin
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 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 761489 c.1683G>A synonymous_variant 1.0
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 1472108 n.263C>T non_coding_transcript_exon_variant 0.1
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.13
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.11
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.31
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.25
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.19
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.16
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.16
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.15
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.19
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.17
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.16
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.16
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.11
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.17
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.23
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.22
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.22
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.22
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.24
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.22
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.22
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.27
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.3
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.28
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.27
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.31
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.17
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.12
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.11
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.12
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.11
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.15
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.13
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.15
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.2
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.19
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.28
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.36
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.39
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.27
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.3
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.28
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726146 c.-47_-46insT upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243246 p.Gly5Val missense_variant 1.0
ethA 4327472 c.2T>G start_lost 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0