TB-Profiler result

Run: ERR4821276
Summary

Run ID: ERR4821276

Sample name:

Date: 2024-10-05T14:02:35.332678

Number of reads: 3003745

Percentage reads mapped: 51.03

Median coverage: 62.0

Strain: lineage3

Spoligotype:

Drug-resistance: Sensitive

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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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7386 p.Ile29Leu missense_variant 0.12 levofloxacin
moxifloxacin
gyrA 7394 c.93T>C synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7406 c.105G>C synonymous_variant 0.11 levofloxacin
moxifloxacin
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
Rv0565c 657081 c.390G>A synonymous_variant 0.98 ethionamide Not assoc w R - Interim
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 760263 p.Met153Leu missense_variant 0.12 rifampicin
rpoB 760266 p.Met154Leu missense_variant 0.12 rifampicin
rpoB 760273 p.Glu156Gly missense_variant 0.12 rifampicin Uncertain significance
rpoB 760298 c.492G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760310 c.504G>C synonymous_variant 0.13 rifampicin
rpoB 760313 c.507G>C synonymous_variant 0.14 rifampicin
rpoB 760991 c.1185G>C synonymous_variant 0.14 rifampicin
rpoB 760997 c.1191G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761006 c.1200C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 761013 p.Val403Ile missense_variant 0.12 rifampicin
rpoB 761027 c.1221A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761046 p.Ile414Val missense_variant 0.14 rifampicin
rpoB 761051 c.1245G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761054 c.1248G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761150 c.1344A>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761162 c.1356G>C synonymous_variant 0.15 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761171 c.1365C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761175 c.1371_1372delGT frameshift_variant 0.16 rifampicin
rpoB 761180 c.1374_1375insGC frameshift_variant 0.15 rifampicin
rpoB 761189 c.1383T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761196 p.Leu464Val missense_variant 0.16 rifampicin
rpoB 761207 c.1401C>T synonymous_variant 0.16 rifampicin
rpoB 761213 c.1407G>C synonymous_variant 0.14 rifampicin
rpoB 761537 c.1731C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761555 c.1749G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 761558 c.1752C>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 761562 p.Ala586Ser missense_variant 0.27 rifampicin
rpoB 761565 p.Met587Leu missense_variant 0.26 rifampicin
rpoB 761570 c.1764T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 761600 c.1794T>C synonymous_variant 0.26 rifampicin
rpoB 761603 c.1797C>T synonymous_variant 0.26 rifampicin
rpoB 761612 c.1806G>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 761627 c.1821C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 762879 p.Met1025Leu missense_variant 0.2 rifampicin Uncertain significance
rpoC 762896 c.-474G>C upstream_gene_variant 0.26 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 762932 c.-438G>C upstream_gene_variant 0.27 rifampicin
rpoC 762947 c.-423C>G upstream_gene_variant 0.27 rifampicin
rpoB 762962 c.3156C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763052 c.-318G>C upstream_gene_variant 0.12 rifampicin
rpoB 763053 c.3247T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763058 c.-312C>G upstream_gene_variant 0.18 rifampicin
rpoB 763070 c.3264T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 763075 p.Thr1090Ile missense_variant 0.22 rifampicin
rpoB 763094 c.3288G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 763126 p.Pro1107Gln missense_variant 0.23 rifampicin
rpoC 763148 c.-222G>C upstream_gene_variant 0.16 rifampicin
rpoC 763660 c.291T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763708 c.339G>C synonymous_variant 0.27 rifampicin
rpoC 763711 c.342G>C synonymous_variant 0.27 rifampicin
rpoC 763714 c.345G>A synonymous_variant 0.26 rifampicin
rpoC 763717 c.348T>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.29 rifampicin
rpoC 763727 p.Leu120Met missense_variant 0.27 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.28 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.25 rifampicin
rpoC 763751 p.Ile128Val missense_variant 0.2 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.16 rifampicin
rpoC 764308 c.939G>C synonymous_variant 0.19 rifampicin
rpoC 764316 p.Ala316Val missense_variant 0.19 rifampicin
rpoC 764320 c.951C>G synonymous_variant 0.22 rifampicin
rpoC 764353 c.984G>C synonymous_variant 0.29 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764371 c.1002G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 764381 c.1012_1013delTCinsAG synonymous_variant 0.36 rifampicin
rpoC 764387 c.1018T>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 764497 c.1128A>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764498 p.Ser377Ala missense_variant 0.24 rifampicin
rpoC 764503 c.1134G>C synonymous_variant 0.31 rifampicin
rpoC 764509 c.1140G>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764521 c.1152T>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764533 c.1164C>T synonymous_variant 0.43 rifampicin
rpoC 764536 c.1167G>T synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 764548 c.1179G>T synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 764549 p.Pro394Thr missense_variant 0.42 rifampicin
rpoC 764561 p.Pro398Ala missense_variant 0.45 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.43 rifampicin
rpoC 764582 p.Leu405Met missense_variant 0.42 rifampicin
rpoC 764611 c.1242G>C synonymous_variant 0.49 rifampicin
rpoC 764632 c.1263T>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764635 c.1266C>G synonymous_variant 0.39 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 0.41 rifampicin Not assoc w R - Interim
rpoC 764660 p.Val431Ile missense_variant 0.36 rifampicin
rpoC 764677 c.1308C>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoC 764683 c.1314G>C synonymous_variant 0.3 rifampicin
rpoC 764692 c.1323C>T synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 764705 p.Leu446Ala missense_variant 0.17 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.12 rifampicin
rpoC 764912 p.Met515Leu missense_variant 0.11 rifampicin
rpoC 764917 c.1548G>C synonymous_variant 0.14 rifampicin
rpoC 764923 c.1554A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764935 c.1566T>C synonymous_variant 0.16 rifampicin
rpoC 764948 c.1579_1581delTTGinsCTC synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764953 c.1584G>C synonymous_variant 0.17 rifampicin
rpoC 764956 c.1587T>C synonymous_variant 0.18 rifampicin
rpoC 764958 p.Glu530Ala missense_variant 0.18 rifampicin
rpoC 764968 c.1599T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 766075 c.2706C>G synonymous_variant 1.0 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
rpsL 781760 c.201T>C synonymous_variant 0.13 streptomycin
rpsL 781794 p.Met79Leu missense_variant 0.15 streptomycin
rpsL 781802 c.243G>C synonymous_variant 0.16 streptomycin
rpsL 781805 c.246G>C synonymous_variant 0.16 streptomycin
rpsL 781808 c.249C>T synonymous_variant 0.15 streptomycin
rpsL 781811 c.252C>A synonymous_variant 0.16 streptomycin
rpsL 781817 c.258G>T synonymous_variant 0.15 streptomycin
rpsL 781829 c.270G>C synonymous_variant 0.12 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.13 streptomycin
rpsL 781838 c.279G>C synonymous_variant 0.12 streptomycin
rpsL 781841 c.282C>T synonymous_variant 0.12 streptomycin
Rv1129c 1253359 c.1176C>T synonymous_variant 1.0 levofloxacin
moxifloxacin
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
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 1473134 n.1289T>C non_coding_transcript_exon_variant 0.54 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.47 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473147 n.1302G>A non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.46 kanamycin
capreomycin
streptomycin Uncertain significance
amikacin
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.64 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473269 n.1424C>T non_coding_transcript_exon_variant 0.5 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.5 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.46 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.43 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.43 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.44 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.6 capreomycin
linezolid
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.64 capreomycin Uncertain significance
linezolid
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.75 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.75 capreomycin Not assoc w R
linezolid Uncertain significance
rpsA 1833709 c.168C>G synonymous_variant 0.12 pyrazinamide
rpsA 1833721 c.180A>G synonymous_variant 0.11 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.11 pyrazinamide
rpsA 1833734 p.Ala65Ser missense_variant 0.12 pyrazinamide
rpsA 1833769 c.228C>G synonymous_variant 0.12 pyrazinamide
rpsA 1833790 c.249T>C synonymous_variant 0.12 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.12 pyrazinamide
rpsA 1833859 c.318C>G synonymous_variant 0.13 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.16 pyrazinamide
rpsA 1833884 p.Thr115Asp missense_variant 0.13 pyrazinamide
rpsA 1833887 p.Ile116Val missense_variant 0.13 pyrazinamide
rpsA 1833893 p.Ala118Lys missense_variant 0.13 pyrazinamide
rpsA 1833896 p.Leu119Ile missense_variant 0.17 pyrazinamide
rpsA 1833907 p.Lys122Asn missense_variant 0.17 pyrazinamide
rpsA 1833912 p.Glu124Gly missense_variant 0.17 pyrazinamide
rpsA 1833915 p.Ala125Val missense_variant 0.17 pyrazinamide Uncertain significance
rpsA 1833921 p.Lys127Thr missense_variant 0.16 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834384 c.843A>G synonymous_variant 0.15 pyrazinamide
rpsA 1834395 p.Arg285Gln missense_variant 0.2 pyrazinamide
rpsA 1834397 p.His286Val missense_variant 0.2 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.33 pyrazinamide
rpsA 1834423 c.882G>T synonymous_variant 0.37 pyrazinamide
rpsA 1834427 p.Ile296Val missense_variant 0.38 pyrazinamide Uncertain significance
rpsA 1834431 p.Val297Ala missense_variant 0.37 pyrazinamide Uncertain significance
rpsA 1834451 c.910_912delTTGinsCTC synonymous_variant 0.39 pyrazinamide
rpsA 1834456 c.915T>C synonymous_variant 0.42 pyrazinamide
rpsA 1834465 c.924T>C synonymous_variant 0.42 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.42 pyrazinamide
rpsA 1834474 c.933C>G synonymous_variant 0.42 pyrazinamide
rpsA 1834482 p.Glu314Ala missense_variant 0.36 pyrazinamide
rpsA 1834486 p.Glu315Asp missense_variant 0.32 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.33 pyrazinamide
rpsA 1834501 c.960G>C synonymous_variant 0.22 pyrazinamide
rpsA 1834513 c.972C>G synonymous_variant 0.13 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 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
folC 2746452 p.Gly383Ser missense_variant 1.0 para-aminosalicylic_acid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.97 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
clpC1 4040024 c.681A>G synonymous_variant 0.12 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.18 pyrazinamide
clpC1 4040063 c.642G>C synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
clpC1 4040066 c.639G>C synonymous_variant 0.26 pyrazinamide
clpC1 4040069 c.636G>C synonymous_variant 0.27 pyrazinamide
clpC1 4040083 p.Thr208Ser missense_variant 0.3 pyrazinamide
clpC1 4040090 c.615T>G synonymous_variant 0.31 pyrazinamide
clpC1 4040096 p.Val203Ile missense_variant 0.28 pyrazinamide
clpC1 4040117 c.588A>G synonymous_variant 0.25 pyrazinamide
clpC1 4040126 c.579C>T synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
clpC1 4040129 c.576C>G synonymous_variant 0.16 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.99 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.97 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
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