TB-Profiler result

Run: ERR108444

Summary

Run ID: ERR108444

Sample name:

Date: 19-10-2023 17:58:50

Number of reads: 4855545

Percentage reads mapped: 96.0

Strain: lineage4.1.2

Drug-resistance: Other


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin R rrs n.888G>A (0.38)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethR p.Phe110Leu (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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H 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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.38 streptomycin
ethR 4327876 p.Phe110Leu missense_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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800889 c.81C>A synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.18
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.2
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.21
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.28
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.31
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.31
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.28
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.26
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.26
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.26
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.23
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.16
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.17
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.15
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.13
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.14
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.14
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.16
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.31
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.33
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.33
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.33
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.35
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.35
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.35
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.34
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.27
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.27
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.26
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.28
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.39
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.38
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.39
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.39
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.36
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.31
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.1
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.1
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.12
rrs 1473191 n.1346C>T non_coding_transcript_exon_variant 0.13
rrs 1473201 n.1356_1357delACinsT non_coding_transcript_exon_variant 0.13
rrs 1473206 n.1361G>A non_coding_transcript_exon_variant 0.13
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.13
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.36
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.5
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.54
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.57
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.57
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.61
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.62
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.73
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.7
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.71
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.7
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.54
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.45
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168303 c.2310G>T synonymous_variant 1.0
PPE35 2169776 p.Phe279Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840263 c.1158C>T synonymous_variant 1.0
rpoA 3877595 p.Gly305Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embC 4242803 p.Val981Leu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0