TB-Profiler result

Run: SRR29096276
Summary

Run ID: SRR29096276

Sample name:

Date: 2025-02-11T10:34:48.203862

Number of reads: 51376

Percentage reads mapped: 51.42

Median coverage: 0.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 0.96
lineage4.9 Euro-American (H37Rv-like) None 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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 Confidence Comment
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 Drugs Confidence
gyrA 7436 c.135C>G synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7442 c.141G>T synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7451 c.150C>G synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7457 c.156T>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7463 c.162G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7466 c.165G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7472 c.171T>C synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7475 c.174A>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7480 p.Phe60Tyr missense_variant 0.93 levofloxacin
moxifloxacin
gyrA 7484 c.183T>C synonymous_variant 0.93 levofloxacin
moxifloxacin
gyrA 7496 c.195C>G synonymous_variant 0.93 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7514 c.213C>G synonymous_variant 0.94 levofloxacin
moxifloxacin
gyrA 7517 c.216G>A synonymous_variant 0.94 levofloxacin
moxifloxacin
gyrA 7520 c.219G>C synonymous_variant 0.94 levofloxacin
moxifloxacin
gyrA 7523 c.222C>A synonymous_variant 0.94 levofloxacin
moxifloxacin
gyrA 7526 c.225G>C synonymous_variant 0.94 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7559 c.258G>A synonymous_variant 0.92 levofloxacin
moxifloxacin
gyrA 7571 c.270G>C synonymous_variant 0.9 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7574 c.273G>C synonymous_variant 0.9 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7742 c.441G>A synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7745 c.444G>A synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7748 c.447A>G synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 9227 c.1926C>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9230 c.1929T>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 9233 c.1932C>A synonymous_variant 1.0 levofloxacin
moxifloxacin Not assoc w R - Interim
gyrA 9236 c.1935G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 9242 c.1941A>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 9252 p.Val651Ile missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9267 p.Asn656Gly missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9281 c.1980C>G synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 9284 c.1983T>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 9296 c.1995T>C synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9299 c.1998G>C synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Glu missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9323 c.2022C>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9335 c.2034G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 9356 c.2055G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 9362 c.2061C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9377 c.2076A>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9383 c.2082T>C synonymous_variant 1.0 levofloxacin
moxifloxacin
ccsA 620541 c.651G>C synonymous_variant 0.82 kanamycin
capreomycin
amikacin
ccsA 620544 c.654G>C synonymous_variant 0.83 kanamycin
capreomycin
amikacin
ccsA 620547 c.657C>G synonymous_variant 0.83 kanamycin
capreomycin
amikacin
ccsA 620559 c.669A>G synonymous_variant 0.89 kanamycin
capreomycin
amikacin
ccsA 620569 p.Gly227Arg missense_variant 0.9 kanamycin
capreomycin
amikacin
ccsA 620604 c.714C>G synonymous_variant 0.88 kanamycin
capreomycin
amikacin
ccsA 620607 c.717T>G synonymous_variant 0.88 kanamycin
capreomycin
amikacin
ccsA 620625 c.735A>C synonymous_variant 0.88 kanamycin
capreomycin
amikacin
ccsA 620631 c.741T>G synonymous_variant 0.88 kanamycin
capreomycin
amikacin
ccsA 620634 c.744C>G synonymous_variant 0.87 kanamycin
capreomycin
amikacin
ccsA 620648 p.Glu253Gly missense_variant 0.95 kanamycin
capreomycin
amikacin
ccsA 620652 c.762C>G synonymous_variant 0.95 kanamycin
capreomycin
amikacin
ccsA 620694 c.804C>G synonymous_variant 0.85 kanamycin
capreomycin
amikacin
ccsA 620698 p.Val270Ile missense_variant 0.85 kanamycin
capreomycin
amikacin
rpoB 761573 c.1767C>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 761606 c.1800C>G synonymous_variant 1.0 rifampicin
rpoB 761612 c.1806G>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 1.0 rifampicin
rpoB 761657 c.1851C>A synonymous_variant 1.0 rifampicin
rpoB 761669 c.1863C>T synonymous_variant 0.95 rifampicin
rpoB 761675 c.1869G>C synonymous_variant 0.94 rifampicin
rpoB 761690 c.1884G>C synonymous_variant 0.93 rifampicin
rpoB 761711 c.1905C>G synonymous_variant 0.92 rifampicin
rpoB 761712 p.Val636Ile missense_variant 0.91 rifampicin
rpoB 761744 c.1938G>A synonymous_variant 0.8 rifampicin
rpoB 761750 c.1944G>C synonymous_variant 0.8 rifampicin
rpoC 765611 p.His748Ser missense_variant 0.9 rifampicin Uncertain significance
rpoC 765625 c.2256C>T synonymous_variant 0.91 rifampicin
rpoC 765628 c.2259G>C synonymous_variant 0.91 rifampicin Not assoc w R - Interim
rpoC 765635 p.Val756Leu missense_variant 0.9 rifampicin
rpoC 765640 c.2271A>G synonymous_variant 0.9 rifampicin
rpoC 765875 p.Val836Ile missense_variant 0.9 rifampicin Uncertain significance
rpoC 765934 c.2565C>T synonymous_variant 1.0 rifampicin
rpoC 765967 c.2598C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765973 c.2604C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765979 c.2610C>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765991 c.2622C>G synonymous_variant 0.92 rifampicin
rpoC 765994 c.2625A>T synonymous_variant 0.92 rifampicin Not assoc w R - Interim
rpoC 766003 c.2634G>C synonymous_variant 0.92 rifampicin
rpoC 766009 c.2640G>C synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 0.81 capreomycin
linezolid
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474263 n.606G>A non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674585 c.384T>C synonymous_variant 0.7 isoniazid
ethionamide
inhA 1674589 p.Met130Leu missense_variant 0.7 isoniazid
ethionamide
inhA 1674597 c.396G>A synonymous_variant 0.7 isoniazid
ethionamide
inhA 1674600 c.399G>C synonymous_variant 0.73 isoniazid
ethionamide
inhA 1674618 c.417C>T synonymous_variant 0.77 isoniazid
ethionamide
inhA 1674624 c.423A>C synonymous_variant 0.77 isoniazid
ethionamide
inhA 1674627 c.426T>C synonymous_variant 0.77 isoniazid
ethionamide
inhA 1674628 p.Ser143Gly missense_variant 0.77 isoniazid
ethionamide
inhA 1674690 c.489C>G synonymous_variant 0.75 isoniazid
ethionamide
inhA 1674693 c.492C>A synonymous_variant 0.75 isoniazid
ethionamide
inhA 1674702 c.501G>A synonymous_variant 0.71 isoniazid
ethionamide
inhA 1674703 c.502T>C synonymous_variant 0.71 isoniazid
ethionamide
inhA 1674714 c.513C>G synonymous_variant 0.77 isoniazid
ethionamide
inhA 1674718 c.517A>C synonymous_variant 0.77 isoniazid
ethionamide
inhA 1674729 c.528G>A synonymous_variant 0.79 isoniazid
ethionamide
tsnR 1853361 c.-245T>C upstream_gene_variant 1.0 linezolid
tsnR 1853370 c.-236_-234delGCAinsTCC upstream_gene_variant 1.0 linezolid
tsnR 1853375 c.-231G>C upstream_gene_variant 1.0 linezolid
tsnR 1853387 c.-219T>G upstream_gene_variant 1.0 linezolid
tsnR 1853390 c.-216G>C upstream_gene_variant 1.0 linezolid
tsnR 1853394 c.-212_-211delCTinsGC upstream_gene_variant 1.0 linezolid
tsnR 1853420 c.-186T>G upstream_gene_variant 1.0 linezolid
tsnR 1853429 c.-177G>C upstream_gene_variant 1.0 linezolid
tsnR 1853432 c.-174G>C upstream_gene_variant 1.0 linezolid
kasA 2517917 c.-198G>T upstream_gene_variant 0.9 isoniazid
kasA 2517926 c.-189G>A upstream_gene_variant 0.9 isoniazid
lpqB 3625054 c.-144C>G upstream_gene_variant 1.0 rifampicin
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3625069 c.-159T>G upstream_gene_variant 1.0 rifampicin
bedaquiline
lpqB 3625072 c.-162G>C upstream_gene_variant 1.0 rifampicin
bedaquiline
lpqB 3625075 c.-165G>C upstream_gene_variant 1.0 rifampicin
bedaquiline
lpqB 3625078 c.-168G>C upstream_gene_variant 1.0 rifampicin
bedaquiline
lpqB 3625087 c.-177C>A upstream_gene_variant 1.0 rifampicin
bedaquiline
mtrB 3625094 p.Glu507Arg missense_variant 1.0 rifampicin
bedaquiline
lpqB 3625099 c.-189C>G upstream_gene_variant 1.0 rifampicin
bedaquiline
lpqB 3625111 c.-201G>C upstream_gene_variant 1.0 rifampicin
bedaquiline
lpqB 3625117 c.-207T>G upstream_gene_variant 1.0 rifampicin
bedaquiline
lpqB 3625123 c.-213T>C upstream_gene_variant 1.0 rifampicin
bedaquiline
lpqB 3625134 c.-224T>C upstream_gene_variant 1.0 rifampicin
bedaquiline
mtrB 3625135 c.1479A>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
lpqB 3625141 c.-231T>C upstream_gene_variant 1.0 rifampicin
bedaquiline
lpqB 3625147 c.-237C>G upstream_gene_variant 1.0 rifampicin
bedaquiline
lpqB 3625161 c.-251T>C upstream_gene_variant 1.0 rifampicin
bedaquiline
mtrB 3625162 c.1452T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
mtrB 3625806 c.808A>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625819 c.795G>A synonymous_variant 0.91 rifampicin Not assoc w R - Interim
bedaquiline
embC 4241002 c.1140G>C synonymous_variant 1.0 ethambutol
embC 4241017 c.1155T>C synonymous_variant 1.0 ethambutol
embC 4241023 c.1161T>C synonymous_variant 1.0 ethambutol
embC 4241024 p.Val388Phe missense_variant 1.0 ethambutol
embC 4241039 p.Asp393Asn missense_variant 1.0 ethambutol
embC 4241047 c.1185C>G synonymous_variant 1.0 ethambutol
embC 4241050 c.1188T>G synonymous_variant 1.0 ethambutol
embC 4241053 c.1191G>T synonymous_variant 1.0 ethambutol
embC 4241071 c.1209C>G synonymous_variant 1.0 ethambutol
embC 4241084 p.Leu408Ala missense_variant 1.0 ethambutol
embC 4241095 c.1233C>T synonymous_variant 1.0 ethambutol
embC 4241125 c.1263G>A synonymous_variant 1.0 ethambutol
embC 4241131 c.1269G>A synonymous_variant 1.0 ethambutol
embC 4241135 p.Val425Leu missense_variant 1.0 ethambutol
embC 4241140 c.1278A>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embC 4241141 p.Ile427Phe missense_variant 1.0 ethambutol
embC 4241158 c.1296T>C synonymous_variant 1.0 ethambutol
embC 4241161 c.1299C>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embC 4241162 p.Leu434Met missense_variant 1.0 ethambutol
embC 4241167 c.1305C>G synonymous_variant 1.0 ethambutol
embC 4241168 c.1306C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embC 4241185 c.1323G>C synonymous_variant 1.0 ethambutol
embC 4241188 c.1326C>G synonymous_variant 1.0 ethambutol
embC 4241194 c.1332C>G synonymous_variant 1.0 ethambutol
embC 4241215 c.1353C>G synonymous_variant 1.0 ethambutol