TB-Profiler result

Run: ERR176464
Summary

Run ID: ERR176464

Sample name:

Date: 24-01-2024 12:25:04

Number of reads: 4140939

Percentage reads mapped: 84.35

Strain: lineage3.1.1

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 (0.46)
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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 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 0.46 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.99
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.19
rrs 1472122 n.277G>A non_coding_transcript_exon_variant 0.24
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.25
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.26
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.35
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.38
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.38
rrs 1472164 n.319G>A non_coding_transcript_exon_variant 0.45
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.46
rrs 1472177 n.332C>T non_coding_transcript_exon_variant 0.46
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.46
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.38
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.36
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.34
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.31
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.22
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.2
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.21
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.13
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.12
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.12
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.13
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.14
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.29
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.32
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.26
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.32
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.33
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.33
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.34
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.34
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.29
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.27
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.31
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.35
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.46
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.45
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.46
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.46
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.43
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.31
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.28
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.44
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.47
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.52
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.54
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.54
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.55
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.65
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.64
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.64
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.64
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.48
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.42
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.2
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A 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
embC 4241562 p.Arg567His missense_variant 0.99
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0