TB-Profiler result

Run: SRR13861500
Summary

Run ID: SRR13861500

Sample name:

Date: 2024-04-16T00:59:09.607688

Number of reads: 407735

Percentage reads mapped: 8.16

Median coverage: 13.0

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 p.Gly442Glu Assoc w R - Interim
c.1327_1329delTTGinsAC Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
c.1345_1347delCTGinsGC 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
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
rpoB 761131 p.Gly442Glu missense_variant 0.39 rifampicin Assoc w R - Interim
rpoB 761133 c.1327_1329delTTGinsAC frameshift_variant&missense_variant 0.41 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpoB 761151 c.1345_1347delCTGinsGC frameshift_variant&missense_variant 0.37 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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 9502 p.Arg734His missense_variant 1.0 levofloxacin
moxifloxacin
Rv0010c 13527 p.Ser11* stop_gained 1.0 isoniazid Uncertain significance
rpoB 761126 c.1320G>T synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoB 761129 c.1323G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoB 761156 c.1350G>C synonymous_variant 0.37 rifampicin
rpoB 761162 c.1356G>C synonymous_variant 0.4 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoB 761168 c.1362C>G synonymous_variant 0.56 rifampicin
rpoB 761178 c.1372_1374delTCAinsAC frameshift_variant&missense_variant 0.42 rifampicin
rpoB 761192 c.1386C>G synonymous_variant 0.4 rifampicin
rpoB 761195 c.1389G>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoB 761196 c.1390_1392delCTGinsTC frameshift_variant&missense_variant 0.4 rifampicin
rpoB 761204 c.1398C>T synonymous_variant 0.4 rifampicin
rpoB 761207 c.1401C>T synonymous_variant 0.4 rifampicin
rpoB 761213 c.1407G>A synonymous_variant 0.4 rifampicin
rpoB 761220 c.1414_1416delTCGinsAC frameshift_variant&missense_variant 0.38 rifampicin
rpoB 761234 c.1428G>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoB 761235 p.Met477Val missense_variant 0.42 rifampicin
rpoB 761239 p.Cys478Tyr missense_variant 0.45 rifampicin
rpoB 762254 c.2448T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 762266 c.2460T>C synonymous_variant 0.3 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
mmpL5 779400 c.-920C>A upstream_gene_variant 1.0 clofazimine
bedaquiline
embR 1417986 c.-639T>A upstream_gene_variant 1.0 ethambutol
rrs 1472865 n.1020C>G non_coding_transcript_exon_variant 0.78 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.33 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.32 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.35 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.37 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.86 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.84 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.48 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1834411 c.870T>C synonymous_variant 0.32 pyrazinamide
rpsA 1834417 c.876G>C synonymous_variant 0.27 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.3 pyrazinamide
rpsA 1834435 c.894G>C synonymous_variant 0.32 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.35 pyrazinamide
rpsA 1834465 c.924T>C synonymous_variant 0.38 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.32 pyrazinamide
rpsA 1834474 c.933C>G synonymous_variant 0.35 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.33 pyrazinamide
rpsA 1834498 c.957C>T synonymous_variant 0.35 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.36 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.4 pyrazinamide
rpsA 1834732 c.1191T>C synonymous_variant 0.4 pyrazinamide
rpsA 1834733 p.Ala398Pro missense_variant 0.4 pyrazinamide
rpsA 1834753 c.1212T>C synonymous_variant 0.43 pyrazinamide
rpsA 1834765 c.1224A>G synonymous_variant 0.38 pyrazinamide
tlyA 1918063 p.Pro42Ala missense_variant 1.0 capreomycin
katG 2155856 p.Thr86Ser missense_variant 1.0 isoniazid
PPE35 2169233 c.1379delT frameshift_variant 1.0 pyrazinamide Uncertain significance
Rv2477c 2783833 c.210G>C synonymous_variant 0.41 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783843 p.Gly67Asp missense_variant 0.35 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783860 p.Asp61Glu missense_variant 0.27 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783863 c.180C>T synonymous_variant 0.27 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2752c 3065376 c.815delT frameshift_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyX 3067731 p.Val72Ala missense_variant 0.94 para-aminosalicylic_acid
thyX 3067825 p.Arg41Gly missense_variant 0.84 para-aminosalicylic_acid
fbiD 3338949 c.-169_-168insT upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
Rv3083 3449768 p.Thr422Lys missense_variant 1.0 ethionamide
lpqB 3623219 c.1692A>G synonymous_variant 1.0 bedaquiline
rifampicin
mtrA 3627790 c.-441A>G upstream_gene_variant 1.0 bedaquiline
rifampicin
alr 3841257 p.His55Leu missense_variant 1.0 cycloserine
rpoA 3877601 p.Gln303* stop_gained 0.87 rifampicin
ethA 4327092 p.Ala128Pro missense_variant 1.0 ethionamide
gid 4408151 p.Leu18Val missense_variant 1.0 streptomycin