TB-Profiler result

Run: SRR3675284
Summary

Run ID: SRR3675284

Sample name:

Date: 2024-03-25T19:37:23.466927

Number of reads: 61115

Percentage reads mapped: 23.5

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 0.99
lineage4.9 Euro-American (H37Rv-like) None 1.0
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
ccsA 620676 c.786C>T synonymous_variant 1.0 capreomycin
amikacin
kanamycin
ccsA 620685 c.795G>A synonymous_variant 1.0 capreomycin Not assoc w R - Interim
amikacin
kanamycin Not assoc w R - Interim
ccsA 620694 c.804C>G synonymous_variant 1.0 capreomycin
amikacin
kanamycin
rpoB 760403 c.597C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 760406 c.600G>C synonymous_variant 1.0 rifampicin
rpoB 762050 c.2244G>A synonymous_variant 1.0 rifampicin
rpoB 762053 c.2247T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762062 c.2256T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762110 c.2304G>C synonymous_variant 1.0 rifampicin
rpoB 762114 p.Ile770Val missense_variant 1.0 rifampicin Uncertain significance
rpoB 762140 c.2334G>C synonymous_variant 1.0 rifampicin
rpoB 762143 c.2337T>C synonymous_variant 1.0 rifampicin
rpoB 762149 c.2343G>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762254 c.2448T>G synonymous_variant 1.0 rifampicin
rpoB 762257 c.2451C>A synonymous_variant 1.0 rifampicin
rpoB 762266 c.2460T>C synonymous_variant 1.0 rifampicin
rpoB 762284 c.2478G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 762989 c.-381G>C upstream_gene_variant 1.0 rifampicin
rpoB 762995 c.3189G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764695 c.1326T>C synonymous_variant 1.0 rifampicin
rpoC 764713 c.1344G>A synonymous_variant 1.0 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764755 c.1386C>T synonymous_variant 1.0 rifampicin
rpoC 764764 c.1395T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764770 c.1401G>A synonymous_variant 1.0 rifampicin
rpoC 764782 c.1413C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764791 c.1422C>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764803 c.1434C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764812 c.1443C>G synonymous_variant 1.0 rifampicin
rpoC 764858 c.1489T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764861 c.1492C>T synonymous_variant 1.0 rifampicin
rpoC 764875 c.1506C>G synonymous_variant 1.0 rifampicin
rpoC 764888 c.1519T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 1.0 rifampicin
rpoC 764902 c.1533C>T synonymous_variant 1.0 rifampicin
rpoC 764918 c.1549_1551delGTGinsAC frameshift_variant&missense_variant 1.0 rifampicin
rpoC 764932 c.1563C>G synonymous_variant 1.0 rifampicin
rpoC 765007 c.1638T>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765019 c.1650A>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765596 p.Lys743Gln missense_variant 1.0 rifampicin
rpoC 765724 c.2355C>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765739 c.2370G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765781 p.Asp804Glu missense_variant 1.0 rifampicin
rpoC 765787 c.2418C>T synonymous_variant 1.0 rifampicin
rpoC 765796 c.2427C>T synonymous_variant 1.0 rifampicin
rpoC 765811 c.2442T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 765814 c.2445A>C synonymous_variant 1.0 rifampicin
rpoC 765823 c.2454C>G synonymous_variant 1.0 rifampicin
rpoC 765826 c.2457T>G synonymous_variant 1.0 rifampicin
rpoC 766492 c.3123T>C synonymous_variant 1.0 rifampicin
rpoC 766518 p.Thr1050Ser missense_variant 1.0 rifampicin
rpoC 766522 c.3153C>A synonymous_variant 1.0 rifampicin
rpoC 766528 c.3159T>G synonymous_variant 1.0 rifampicin
rpoC 766534 c.3165C>G synonymous_variant 1.0 rifampicin
rpoC 766570 c.3201T>C synonymous_variant 1.0 rifampicin
rpoC 766585 c.3216T>C synonymous_variant 1.0 rifampicin
rpoC 766597 c.3228C>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 766607 p.Ile1080Leu missense_variant 1.0 rifampicin
fbiC 1305276 c.2346G>T synonymous_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1305282 c.2352T>C synonymous_variant 1.0 clofazimine
pretomanid
delamanid
rpsA 1833916 c.375C>G synonymous_variant 1.0 pyrazinamide
rpsA 1833922 c.381G>A synonymous_variant 1.0 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 1.0 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 1.0 pyrazinamide
rpsA 1833988 c.447C>G synonymous_variant 1.0 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834285 c.744G>A synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834297 c.756C>G synonymous_variant 1.0 pyrazinamide
rpsA 1834303 c.762T>C synonymous_variant 1.0 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 1.0 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834351 c.810G>A synonymous_variant 1.0 pyrazinamide
rpsA 1834366 c.825A>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834381 c.840G>A synonymous_variant 1.0 pyrazinamide
rpsA 1834411 c.870T>G synonymous_variant 1.0 pyrazinamide
rpsA 1834414 c.873C>T synonymous_variant 1.0 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 1.0 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 1.0 pyrazinamide
rpsA 1834456 c.915T>G synonymous_variant 1.0 pyrazinamide
rpsA 1834465 c.924T>C synonymous_variant 1.0 pyrazinamide
rpsA 1834519 c.978G>C synonymous_variant 1.0 pyrazinamide
rpsA 1834520 p.Ala327Ser missense_variant 1.0 pyrazinamide
rpsA 1834555 c.1014T>C synonymous_variant 1.0 pyrazinamide
rpsA 1834557 p.Ala339Gly missense_variant 1.0 pyrazinamide
rpsA 1834561 c.1020C>G synonymous_variant 1.0 pyrazinamide
rpsA 1834570 p.Asp343Glu missense_variant 1.0 pyrazinamide
rpsA 1834572 p.Ala344Val missense_variant 1.0 pyrazinamide
rpsA 1834603 c.1062G>A synonymous_variant 1.0 pyrazinamide
Rv2752c 3065073 c.1119C>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
moxifloxacin
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv2752c 3065087 c.1105A>C synonymous_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid Not assoc w R - Interim
Rv2752c 3065088 c.1104A>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
moxifloxacin
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv2752c 3065094 c.1098C>T synonymous_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065097 c.1095C>T synonymous_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065106 c.1086C>T synonymous_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065109 c.1081_1083delAGAinsCC frameshift_variant&missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv2752c 3065127 c.1065G>T synonymous_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065131 p.Ala354Glu missense_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3065133 c.1059T>C synonymous_variant 1.0 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
rpoA 3878343 c.165C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 1.0 rifampicin
rpoA 3878364 c.144A>C synonymous_variant 1.0 rifampicin
rpoA 3878385 c.123C>G synonymous_variant 1.0 rifampicin
rpoA 3878391 c.117T>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3878400 c.108T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3878403 c.105C>T synonymous_variant 1.0 rifampicin
rpoA 3878406 c.102G>C synonymous_variant 1.0 rifampicin
rpoA 3878409 c.99C>G synonymous_variant 1.0 rifampicin
clpC1 4040582 c.123G>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4040585 c.120A>G synonymous_variant 1.0 pyrazinamide
clpC1 4040588 c.117T>C synonymous_variant 1.0 pyrazinamide
clpC1 4040600 c.105A>G synonymous_variant 1.0 pyrazinamide
clpC1 4040603 c.102T>G synonymous_variant 1.0 pyrazinamide
clpC1 4040606 c.99T>C synonymous_variant 1.0 pyrazinamide
clpC1 4040644 c.61A>C synonymous_variant 1.0 pyrazinamide
embB 4248226 c.1713G>C synonymous_variant 1.0 ethambutol