TB-Profiler result

Run: SRR13861553
Summary

Run ID: SRR13861553

Sample name:

Date: 2024-10-05T10:19:39.830482

Number of reads: 2339214

Percentage reads mapped: 58.53

Median coverage: 80.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

Download CSV Download TXT Download JSON
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 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 pepQ c.248_249insA Assoc w R - Interim
para-aminosalicylic_acid
delamanid
bedaquiline pepQ c.248_249insA Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
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
pepQ 2860170 c.248_249insA frameshift_variant 0.97 bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
clofazimine Assoc w R - Interim
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
gyrB 4992 c.-248_-247insT upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrA 7018 c.-284G>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
mshA 576668 c.1322dupA frameshift_variant&stop_gained 1.0 isoniazid Uncertain significance
ethionamide Uncertain significance
Rv0565c 656976 c.495G>A synonymous_variant 1.0 ethionamide
Rv0565c 657336 c.135G>C synonymous_variant 0.97 ethionamide
rpoB 760181 c.375T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760223 c.417T>C synonymous_variant 0.15 rifampicin
rpoB 760235 c.429T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761094 c.1288C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761097 c.1291_1292delAGinsTC synonymous_variant 0.15 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.17 rifampicin
rpoB 761133 c.1327_1329delTTGinsCTC synonymous_variant 0.17 rifampicin
rpoB 761150 c.1344A>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761165 c.1359G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761168 c.1362C>G synonymous_variant 0.18 rifampicin
rpoB 761171 c.1365C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761183 c.1377T>G synonymous_variant 0.19 rifampicin
rpoB 761189 c.1383T>G synonymous_variant 0.19 rifampicin
rpoB 761222 c.1416G>C synonymous_variant 0.21 rifampicin
rpoB 761249 c.1443A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761255 c.1449T>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761261 c.1455G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 765100 c.1731G>C synonymous_variant 0.95 rifampicin
rpoC 766408 c.3039C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
mmpL5 776059 p.Val808Met missense_variant 0.95 bedaquiline
clofazimine
fbiC 1304599 p.Ile557Phe missense_variant 0.94 pretomanid
delamanid
clofazimine
embR 1417348 c.-1A>T upstream_gene_variant 1.0 ethambutol
rrl 1473631 n.-27T>C upstream_gene_variant 1.0 capreomycin
linezolid
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1833855 p.Lys105Thr missense_variant 0.9 pyrazinamide
rpsA 1834222 c.681T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834225 c.684C>G synonymous_variant 0.15 pyrazinamide
rpsA 1834240 c.699T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834297 c.756C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
tlyA 1917702 c.-238G>C upstream_gene_variant 1.0 capreomycin
bacA 2064233 c.495dupG frameshift_variant 1.0 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
katG 2156789 c.-678G>T upstream_gene_variant 1.0 isoniazid
PPE35 2170030 p.Met195Leu missense_variant 1.0 pyrazinamide
kasA 2518276 p.Trp54* stop_gained 0.97 isoniazid
kasA 2518352 p.Met80Val missense_variant 1.0 isoniazid
eis 2714478 c.855C>A synonymous_variant 1.0 kanamycin
amikacin
Rv2477c 2783586 p.Ala153Pro missense_variant 0.13 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2681 2997465 p.Val243Leu missense_variant 1.0 capreomycin
Rv2752c 3065335 p.Leu286Arg missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
mtrB 3626280 p.Thr112Pro missense_variant 1.0 rifampicin
bedaquiline
mtrB 3626858 c.-245A>G upstream_gene_variant 0.13 rifampicin
bedaquiline
mtrB 3626903 c.-290T>C upstream_gene_variant 0.14 rifampicin
bedaquiline
mtrB 3626930 c.-317A>G upstream_gene_variant 0.15 rifampicin
bedaquiline
fbiA 3640236 c.-307T>A upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
fbiA 3640307 c.-236C>G upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
fbiB 3641019 c.-516G>A upstream_gene_variant 1.0 pretomanid
delamanid
clofazimine
fbiB 3641941 p.Leu136Gln missense_variant 1.0 pretomanid
delamanid
clofazimine
rpoA 3877743 c.765T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877839 c.669G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3879121 c.-614T>G upstream_gene_variant 0.14 rifampicin
clpC1 4038851 c.1854G>A synonymous_variant 0.13 pyrazinamide
clpC1 4038932 c.1773G>C synonymous_variant 0.15 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.13 pyrazinamide
clpC1 4038997 c.1708T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4039097 c.1608G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.16 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.16 pyrazinamide
clpC1 4039169 p.Glu512Asp missense_variant 0.15 pyrazinamide
clpC1 4039172 c.1533A>G synonymous_variant 0.16 pyrazinamide
clpC1 4039178 c.1527G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039187 c.1518G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039226 c.1479T>C synonymous_variant 0.13 pyrazinamide Not assoc w R - Interim
clpC1 4039268 c.1437C>G synonymous_variant 0.17 pyrazinamide
clpC1 4039274 c.1431G>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4039286 c.1419T>C synonymous_variant 0.18 pyrazinamide
clpC1 4039289 c.1416T>C synonymous_variant 0.16 pyrazinamide
clpC1 4039295 c.1410A>C synonymous_variant 0.17 pyrazinamide
clpC1 4039298 c.1407T>C synonymous_variant 0.17 pyrazinamide
clpC1 4039319 c.1386T>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4039322 c.1383T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039328 c.1377A>G synonymous_variant 0.16 pyrazinamide
clpC1 4039334 c.1371G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039337 p.Thr456Gln missense_variant 0.15 pyrazinamide
clpC1 4039484 c.1221T>G synonymous_variant 0.14 pyrazinamide
clpC1 4039517 c.1188C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039524 p.Phe394Tyr missense_variant 0.16 pyrazinamide
clpC1 4039526 c.1179G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039547 c.1158C>G synonymous_variant 0.14 pyrazinamide
clpC1 4039553 c.1152C>G synonymous_variant 0.14 pyrazinamide
glpK 4139862 c.-107C>A upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4240789 c.927T>C synonymous_variant 0.14 ethambutol
embC 4240819 c.957A>G synonymous_variant 0.15 ethambutol
embC 4240825 c.963G>A synonymous_variant 0.15 ethambutol
embC 4240831 c.969T>G synonymous_variant 0.15 ethambutol
embC 4241292 p.Leu477Gln missense_variant 1.0 ethambutol Uncertain significance
embC 4242011 p.Leu717Val missense_variant 1.0 ethambutol
embB 4248720 p.Gly736Ala missense_variant 1.0 ethambutol
embB 4249676 p.Arg1055Cys missense_variant 1.0 ethambutol
aftB 4267927 p.Ala304Ser missense_variant 0.96 ethambutol Uncertain significance