TB-Profiler result

Run: SRR13861553
Summary

Run ID: SRR13861553

Sample name:

Date: 2024-04-14T17:22:59.123406

Number of reads: 2339214

Percentage reads mapped: 58.53

Median coverage: 80.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: RR-TB

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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 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB c.1327_1329delTTGinsCC Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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
rpoB 761133 c.1327_1329delTTGinsCC frameshift_variant&missense_variant 0.17 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
pepQ 2860170 c.248_249insA frameshift_variant 0.97 clofazimine Assoc w R - Interim
bedaquiline Assoc w R - Interim Includes data from one site that only submitted resistant strains, which may have inflated the PPV
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 ethionamide Uncertain significance
isoniazid 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 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 clofazimine
bedaquiline
fbiC 1304599 p.Ile557Phe missense_variant 0.94 clofazimine
pretomanid
delamanid
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 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin 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 amikacin
kanamycin
Rv2477c 2783586 p.Ala153Pro missense_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2681 2997465 p.Val243Leu missense_variant 1.0 capreomycin
Rv2752c 3065335 p.Leu286Arg missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
mtrB 3626280 p.Thr112Pro missense_variant 1.0 bedaquiline
rifampicin
mtrB 3626858 c.-245A>G upstream_gene_variant 0.13 bedaquiline
rifampicin
mtrB 3626903 c.-290T>C upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3626930 c.-317A>G upstream_gene_variant 0.15 bedaquiline
rifampicin
fbiA 3640236 c.-307T>A upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
fbiA 3640307 c.-236C>G upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
fbiB 3641019 c.-516G>A upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
fbiB 3641941 p.Leu136Gln missense_variant 1.0 clofazimine
pretomanid
delamanid
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 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
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