TB-Profiler result

Run: SRR29096882
Summary

Run ID: SRR29096882

Sample name:

Date: 2024-09-26T19:26:56.549448

Number of reads: 57199

Percentage reads mapped: 28.61

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 1.0
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
dnaA 1278 c.1278T>C synonymous_variant 1.0 isoniazid
dnaA 1281 c.1281C>G synonymous_variant 1.0 isoniazid
dnaA 1287 c.1287A>G synonymous_variant 1.0 isoniazid
dnaA 1293 c.1293T>G synonymous_variant 1.0 isoniazid
dnaA 1317 c.1317A>G synonymous_variant 0.7 isoniazid
dnaA 1329 c.1329A>C synonymous_variant 1.0 isoniazid
dnaA 1338 c.1338T>C synonymous_variant 1.0 isoniazid
dnaA 1341 c.1341G>C synonymous_variant 1.0 isoniazid
gyrA 7523 c.222C>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7526 c.225G>C synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7532 c.231T>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7541 c.240C>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7547 c.246C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7565 c.264C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7592 c.291G>C synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7607 c.306C>G synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7619 c.318C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7631 c.330G>C synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7637 c.336C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
gyrA 7652 c.351C>T 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
mshA 575734 c.387T>G synonymous_variant 1.0 ethionamide
isoniazid
mshA 575737 c.390T>C synonymous_variant 1.0 ethionamide
isoniazid
mshA 575744 p.Ala133Thr missense_variant 1.0 ethionamide
isoniazid Uncertain significance
mshA 575756 c.409C>T synonymous_variant 0.93 ethionamide
isoniazid
mshA 575761 c.414C>G synonymous_variant 1.0 ethionamide
isoniazid
mshA 575771 p.Val142Thr missense_variant 1.0 ethionamide
isoniazid
mshA 575779 c.432A>G synonymous_variant 0.87 ethionamide
isoniazid
mshA 575782 c.435G>C synonymous_variant 1.0 ethionamide
isoniazid
mshA 575785 c.438T>C synonymous_variant 1.0 ethionamide
isoniazid
mshA 575795 c.448_450delATCinsGG frameshift_variant&missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 575842 c.495G>C synonymous_variant 1.0 ethionamide
isoniazid
mshA 575843 p.Arg166Ser missense_variant 0.77 ethionamide
isoniazid
mshA 575864 c.517T>C synonymous_variant 1.0 ethionamide
isoniazid
nusG 734439 c.186C>G synonymous_variant 1.0 rifampicin
nusG 734442 c.189G>A synonymous_variant 1.0 rifampicin
nusG 734451 c.198G>C synonymous_variant 1.0 rifampicin
nusG 734454 c.201A>G synonymous_variant 1.0 rifampicin
nusG 734460 c.207G>C synonymous_variant 1.0 rifampicin
nusG 734472 c.219T>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
nusG 734475 c.222T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
nusG 734481 c.228C>T synonymous_variant 1.0 rifampicin
nusG 734499 c.246G>C synonymous_variant 1.0 rifampicin
nusG 734532 c.279A>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 760646 c.840C>G synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rpoB 760655 c.849A>G synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rpoB 760658 c.852G>A synonymous_variant 0.9 rifampicin
rpoB 760661 c.855A>C synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rpoB 760670 c.864G>C synonymous_variant 0.92 rifampicin
rpoB 760674 c.868T>C synonymous_variant 0.93 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.93 rifampicin Not assoc w R - Interim
rpoB 760683 c.877T>C synonymous_variant 0.93 rifampicin Not assoc w R - Interim
rpoB 760721 c.915C>G synonymous_variant 1.0 rifampicin
rpoB 760730 c.924T>C synonymous_variant 0.97 rifampicin Not assoc w R - Interim
rpoB 760748 c.942C>G synonymous_variant 0.94 rifampicin
rpoB 760751 c.945G>C synonymous_variant 0.97 rifampicin
rpoB 760754 c.948G>C synonymous_variant 0.97 rifampicin
rpoB 760755 c.949_951delCATinsAC frameshift_variant&missense_variant 0.94 rifampicin
rpoB 760759 p.Val318Ala missense_variant 0.97 rifampicin
rpoB 760764 p.Glu320Gln missense_variant 0.97 rifampicin
rpoB 760769 c.963C>G synonymous_variant 0.97 rifampicin
rpoB 760793 c.987A>G synonymous_variant 0.97 rifampicin
rpoB 760805 c.999G>C synonymous_variant 0.96 rifampicin
rpoB 760817 c.1011A>G synonymous_variant 0.96 rifampicin
rpoB 760820 c.1014T>C synonymous_variant 0.96 rifampicin
rpoB 760826 c.1020C>G synonymous_variant 0.96 rifampicin Not assoc w R - Interim
rpoB 760830 c.1024T>C synonymous_variant 0.96 rifampicin Not assoc w R - Interim
rpoB 760841 c.1035T>C synonymous_variant 0.95 rifampicin Not assoc w R - Interim
rpoB 760859 c.1053T>C synonymous_variant 0.93 rifampicin
rpoB 760862 c.1056G>C synonymous_variant 0.91 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.92 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.92 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 0.92 rifampicin
rpoB 761666 c.1860G>C synonymous_variant 0.93 rifampicin
rpoB 761669 c.1863C>T synonymous_variant 0.93 rifampicin
rpoB 761675 c.1869G>C synonymous_variant 0.95 rifampicin
rpoB 761687 c.1881C>T synonymous_variant 0.95 rifampicin
rpoB 761690 c.1884G>C synonymous_variant 0.95 rifampicin
rpoB 761693 c.1887G>C synonymous_variant 0.95 rifampicin
rpoB 761708 c.1902C>T synonymous_variant 0.94 rifampicin
rpoB 761718 p.Ala638Ser missense_variant 0.94 rifampicin
rpoB 761736 p.Ile644Val missense_variant 0.94 rifampicin Uncertain significance
rpoB 761747 c.1941G>C synonymous_variant 0.94 rifampicin
rpoB 761765 c.1959T>C synonymous_variant 0.9 rifampicin
mmpL5 775862 c.2619G>C synonymous_variant 0.9 clofazimine
bedaquiline
mmpL5 775946 c.2535C>G synonymous_variant 0.6 clofazimine
bedaquiline
rpsL 781916 c.357T>C synonymous_variant 0.9 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.91 streptomycin Uncertain significance
fbiC 1304613 c.1683T>C synonymous_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1304628 c.1698G>T synonymous_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1304634 c.1704C>G synonymous_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1304640 c.1710A>C synonymous_variant 1.0 clofazimine
pretomanid
delamanid
fbiC 1304643 c.1713G>A synonymous_variant 1.0 clofazimine
pretomanid
delamanid
sigE 1364839 c.427T>C synonymous_variant 0.8 pyrazinamide
rrs 1472847 n.1002G>C non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472848 n.1003T>A non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472849 n.1004C>G non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472859 n.1014G>T non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 1.0 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rpoA 3877818 c.690A>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3877839 c.669G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3877848 c.660C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3877857 c.651G>A synonymous_variant 1.0 rifampicin
rpoA 3877866 c.642G>C synonymous_variant 1.0 rifampicin
rpoA 3877875 c.633T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3877887 c.621G>C synonymous_variant 1.0 rifampicin
rpoA 3877893 c.615C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3877905 c.603A>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3877908 c.600T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3877926 c.582G>C synonymous_variant 1.0 rifampicin
rpoA 3877929 c.579C>T synonymous_variant 1.0 rifampicin
rpoA 3877962 c.546G>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3877971 p.Asp179Glu missense_variant 1.0 rifampicin Uncertain significance
clpC1 4039361 c.1344C>A synonymous_variant 0.82 pyrazinamide
clpC1 4039382 c.1323C>G synonymous_variant 0.86 pyrazinamide
clpC1 4039391 c.1314T>G synonymous_variant 0.85 pyrazinamide
clpC1 4039394 c.1311G>C synonymous_variant 0.85 pyrazinamide
clpC1 4039397 c.1308A>G synonymous_variant 0.86 pyrazinamide
clpC1 4039409 c.1296T>C synonymous_variant 0.87 pyrazinamide
clpC1 4039412 c.1293T>G synonymous_variant 0.87 pyrazinamide
clpC1 4039415 p.Glu430Asp missense_variant 0.87 pyrazinamide Uncertain significance
clpC1 4039430 c.1275T>C synonymous_variant 0.88 pyrazinamide
clpC1 4039442 c.1263A>G synonymous_variant 0.88 pyrazinamide
clpC1 4039454 c.1251A>T synonymous_variant 0.88 pyrazinamide
clpC1 4039463 c.1242C>G synonymous_variant 0.88 pyrazinamide
clpC1 4039466 c.1239T>C synonymous_variant 0.88 pyrazinamide
clpC1 4039469 c.1236T>C synonymous_variant 0.88 pyrazinamide
clpC1 4039481 c.1224T>C synonymous_variant 0.93 pyrazinamide
clpC1 4039487 c.1218G>C synonymous_variant 0.91 pyrazinamide
embB 4247866 c.1353G>C synonymous_variant 0.9 ethambutol
embB 4247869 c.1356G>C synonymous_variant 0.9 ethambutol
embB 4247887 c.1374C>T synonymous_variant 0.9 ethambutol Not assoc w R - Interim
embB 4247893 c.1380C>T synonymous_variant 0.9 ethambutol
embB 4247905 c.1392G>C synonymous_variant 0.9 ethambutol Not assoc w R - Interim
embB 4247909 c.1396T>C synonymous_variant 0.9 ethambutol
embB 4247917 c.1404C>G synonymous_variant 0.9 ethambutol
embB 4247920 c.1407T>C synonymous_variant 0.9 ethambutol
embB 4247922 p.His470Arg missense_variant 0.9 ethambutol
embB 4247927 c.1414_1416delCTGinsGC frameshift_variant&missense_variant 0.9 ethambutol
embB 4247930 p.Val473Leu missense_variant 0.9 ethambutol
embB 4247936 p.Thr475Val missense_variant 0.9 ethambutol
embB 4247940 p.Leu476Trp missense_variant 0.9 ethambutol
embB 4247952 p.Ser480Leu missense_variant 0.9 ethambutol Uncertain significance
embB 4247957 p.Met482Leu missense_variant 0.9 ethambutol
embB 4247965 c.1452C>G synonymous_variant 0.9 ethambutol
embB 4247968 c.1455C>A synonymous_variant 0.9 ethambutol
embB 4247974 c.1461C>A synonymous_variant 0.91 ethambutol
embB 4247977 c.1464C>G synonymous_variant 0.91 ethambutol
embB 4248085 c.1572T>C synonymous_variant 0.9 ethambutol
embB 4248097 c.1584C>G synonymous_variant 0.9 ethambutol
embB 4248106 c.1593C>G synonymous_variant 0.73 ethambutol
embB 4248118 c.1605T>C synonymous_variant 0.92 ethambutol
embB 4248130 c.1617G>C synonymous_variant 0.92 ethambutol
embB 4248142 c.1629T>C synonymous_variant 1.0 ethambutol
embB 4248143 c.1630_1632delTTGinsAC frameshift_variant&missense_variant 1.0 ethambutol
embB 4248157 c.1644A>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4248158 p.Cys549Ser missense_variant 1.0 ethambutol
embB 4248167 p.Thr552Ala missense_variant 1.0 ethambutol
embB 4248170 p.Ala553Ser missense_variant 1.0 ethambutol
embB 4248173 p.Val554Leu missense_variant 1.0 ethambutol
embB 4248199 c.1686A>G synonymous_variant 1.0 ethambutol
embB 4248200 p.Ile563Val missense_variant 1.0 ethambutol
embB 4248206 c.1693_1695delAGCinsGT frameshift_variant&missense_variant 1.0 ethambutol
embB 4248220 c.1707A>G synonymous_variant 0.9 ethambutol Not assoc w R - Interim