TB-Profiler result

Run: ERR4815556
Summary

Run ID: ERR4815556

Sample name:

Date: 2024-10-05T09:57:32.611110

Number of reads: 824746

Percentage reads mapped: 68.62

Median coverage: 26.0

Strain: lineage3

Spoligotype:

Drug-resistance: RR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 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.Ser441Ala Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1402C>A Uncertain significance Mutation from literature
capreomycin rrs n.1402C>A Uncertain significance Mutation from literature
kanamycin rrs n.1402C>A Uncertain significance Mutation from literature
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 761127 p.Ser441Ala missense_variant 0.26 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.82 amikacin Uncertain significance Mutation from literature
capreomycin Uncertain significance Mutation from literature
kanamycin Uncertain significance Mutation from literature
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 410 p.Ala137Asp missense_variant 1.0 isoniazid Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 574795 c.-553A>G upstream_gene_variant 1.0 isoniazid Uncertain significance
ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 761084 c.1278C>A synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761088 c.1282_1283delAGinsTC synonymous_variant 0.21 rifampicin
rpoB 761097 c.1291_1292delAGinsTC synonymous_variant 0.21 rifampicin
rpoB 761102 c.1296A>G synonymous_variant 0.24 rifampicin
rpoB 761126 c.1320G>C synonymous_variant 0.26 rifampicin
rpoB 761132 c.1326G>T synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 761156 c.1350G>C synonymous_variant 0.29 rifampicin
rpoB 761207 c.1401C>T synonymous_variant 0.3 rifampicin
rpoB 761213 c.1407G>C synonymous_variant 0.29 rifampicin
rpoB 761219 c.1413G>C synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 761234 c.1428G>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 762929 c.3123G>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 762938 c.-432G>C upstream_gene_variant 0.27 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763528 c.159G>T synonymous_variant 0.31 rifampicin
rpoC 763531 c.162G>C synonymous_variant 0.31 rifampicin Not assoc w R
rpoC 763534 c.165T>C synonymous_variant 0.3 rifampicin
rpoC 763537 c.168C>G synonymous_variant 0.33 rifampicin
rpoC 763546 c.177A>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 763578 p.Phe70Tyr missense_variant 0.38 rifampicin
rpoC 763609 c.240C>G synonymous_variant 0.41 rifampicin
rpoC 763615 c.246G>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 763618 c.249C>G synonymous_variant 0.45 rifampicin
rpoC 763621 c.252C>T synonymous_variant 0.46 rifampicin
rpoC 763642 c.273G>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>C synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>T synonymous_variant 0.43 rifampicin
rpoC 763672 c.303C>G synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 763699 c.330G>T synonymous_variant 0.33 rifampicin
rpoC 763708 c.339G>C synonymous_variant 0.31 rifampicin
rpoC 763709 c.340C>T synonymous_variant 0.31 rifampicin
rpoC 763714 c.345G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 763729 c.360G>C synonymous_variant 0.29 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.29 rifampicin
rpoC 763735 c.366G>C synonymous_variant 0.28 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.27 rifampicin
rpoC 764347 c.978G>C synonymous_variant 0.26 rifampicin
rpoC 764359 c.990C>G synonymous_variant 0.35 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 764377 c.1008C>G synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 764387 c.1018_1020delTTGinsCTC synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 764398 c.1029G>C synonymous_variant 0.4 rifampicin
rpoC 764404 c.1035C>T synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 764405 c.1036A>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 764428 c.1059G>C synonymous_variant 0.48 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 764435 c.1066_1068delAGGinsCGT synonymous_variant 0.41 rifampicin
rpoC 764441 p.Ile358Leu missense_variant 0.42 rifampicin
rpoC 764446 c.1077T>C synonymous_variant 0.41 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.39 rifampicin
rpoC 764455 c.1086G>C synonymous_variant 0.39 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764470 c.1101C>G synonymous_variant 0.42 rifampicin
rpoC 764485 c.1116G>C synonymous_variant 0.46 rifampicin
rpoC 764497 c.1128A>G synonymous_variant 0.49 rifampicin Not assoc w R - Interim
rpoC 764498 p.Ser377Ala missense_variant 0.55 rifampicin
rpoC 764507 p.Ala380Ser missense_variant 0.54 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 764524 c.1155C>T synonymous_variant 0.41 rifampicin
rpoC 764536 c.1167G>T synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 764545 c.1176C>G synonymous_variant 0.46 rifampicin
rpoC 764548 c.1179G>T synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 764561 p.Pro398Ala missense_variant 0.43 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.43 rifampicin Not assoc w R - Interim
rpoC 764572 c.1203G>C synonymous_variant 0.41 rifampicin
rpoC 764575 c.1206T>G synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.39 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.39 rifampicin
rpoC 764602 c.1233C>A synonymous_variant 0.48 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>C synonymous_variant 0.52 rifampicin
rpoC 764623 c.1254C>G synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 764635 c.1266C>G synonymous_variant 0.42 rifampicin
rpoC 764677 c.1308C>G synonymous_variant 0.51 rifampicin Not assoc w R - Interim
rpoC 764706 p.Leu446Gln missense_variant 0.44 rifampicin Uncertain significance
rpoC 764746 c.1377G>C synonymous_variant 0.44 rifampicin
rpoC 764758 c.1389C>G synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 764767 c.1398G>T synonymous_variant 0.4 rifampicin
rpoC 764780 c.1411_1412delAGinsTC synonymous_variant 0.4 rifampicin
rpoC 764804 p.Gln479Tyr missense_variant 0.36 rifampicin
rpoC 764809 c.1440C>T synonymous_variant 0.34 rifampicin Not assoc w R
rpoC 764815 c.1446A>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472289 n.444T>C non_coding_transcript_exon_variant 0.8 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472290 n.445C>G non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472313 n.468delGinsAA non_coding_transcript_exon_variant 0.8 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472315 n.470T>G non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472324 n.479G>C non_coding_transcript_exon_variant 0.8 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.73 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1472338 n.493A>G non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.73 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472880 n.1035G>A non_coding_transcript_exon_variant 0.82 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.9 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.92 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473022 n.1177G>A non_coding_transcript_exon_variant 0.47 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.91 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.91 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.93 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.94 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.95 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.91 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.91 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473129 n.1284C>T non_coding_transcript_exon_variant 0.91 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.92 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.89 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.8 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.8 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475778 n.2121G>A non_coding_transcript_exon_variant 0.82 capreomycin
linezolid
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.92 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.92 capreomycin Uncertain significance
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.86 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.86 capreomycin Not assoc w R
linezolid Uncertain significance
tsnR 1854300 p.Leu232Pro missense_variant 0.96 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 1.0 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
fbiB 3642759 p.Arg409Ser missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
clpC1 4039730 c.975C>G synonymous_variant 0.21 pyrazinamide
clpC1 4039748 c.957G>C synonymous_variant 0.23 pyrazinamide
clpC1 4039751 c.954A>G synonymous_variant 0.24 pyrazinamide
clpC1 4039757 c.948A>G synonymous_variant 0.22 pyrazinamide
clpC1 4039766 c.939T>C synonymous_variant 0.24 pyrazinamide
clpC1 4039769 c.936C>G synonymous_variant 0.24 pyrazinamide
clpC1 4039773 p.Lys311Met missense_variant 0.24 pyrazinamide
clpC1 4039775 c.930G>C synonymous_variant 0.24 pyrazinamide
clpC1 4039778 c.927A>G synonymous_variant 0.24 pyrazinamide
clpC1 4039781 c.924G>C synonymous_variant 0.24 pyrazinamide
clpC1 4039850 c.855T>C synonymous_variant 0.33 pyrazinamide
clpC1 4039865 c.840T>G synonymous_variant 0.37 pyrazinamide
clpC1 4039928 c.775_777delAGCinsTCT synonymous_variant 0.35 pyrazinamide
clpC1 4039943 c.762G>C synonymous_variant 0.33 pyrazinamide
clpC1 4039946 c.759A>C synonymous_variant 0.3 pyrazinamide
clpC1 4039949 c.756G>C synonymous_variant 0.3 pyrazinamide
clpC1 4039952 c.753T>C synonymous_variant 0.3 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4139183 c.572dupG frameshift_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R