TB-Profiler result

Run: ERR2706950
Summary

Run ID: ERR2706950

Sample name:

Date: 2024-06-18T11:31:04.313845

Number of reads: 5703700

Percentage reads mapped: 91.06

Median coverage: 165.0

Strain: lineage5.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage5.2 West-Africa 1 RD711 0.99
lineage5 West-Africa 1 RD711 0.97
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
pyrazinamide pncA p.Val180Gly Assoc w R
streptomycin rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid folC p.Glu153Gly Mutation from literature
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.93 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288703 p.Val180Gly missense_variant 0.99 pyrazinamide Assoc w R
folC 2747141 p.Glu153Gly missense_variant 0.99 para-aminosalicylic_acid Mutation from literature
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol 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
gyrB 5124 c.-116T>C upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 6238 c.999G>A synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6253 c.1014G>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrB 6265 c.1026C>T synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6292 c.1053G>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrB 6319 c.1080G>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrB 6446 p.Ala403Ser missense_variant 0.98 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrA 7362 p.Glu21Gln missense_variant 0.99 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 9143 c.1842T>C synonymous_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
gyrA 9566 c.2265C>T synonymous_variant 0.99 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
Rv0010c 13579 c.-21G>A upstream_gene_variant 0.99 isoniazid Uncertain significance
fgd1 491259 c.477T>C synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
hadA 731750 c.-180G>C upstream_gene_variant 0.97 isoniazid
hadA 732110 p.Cys61Gly missense_variant 1.0 isoniazid Uncertain significance
rpoB 761054 c.1248G>A synonymous_variant 0.13 rifampicin
rpoB 761060 c.1254C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761165 c.1359G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761183 c.1377T>G synonymous_variant 0.14 rifampicin
rpoB 761189 c.1383T>G synonymous_variant 0.15 rifampicin
rpoB 761195 c.1389G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761198 c.1392G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761222 c.1416G>C synonymous_variant 0.13 rifampicin
rpoB 762114 c.2308_2310delATCinsGG frameshift_variant&missense_variant 0.15 rifampicin
rpoB 762122 c.2316C>T synonymous_variant 0.14 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>T synonymous_variant 0.16 rifampicin
rpoB 762254 c.2448T>G synonymous_variant 0.15 rifampicin
rpoB 762338 c.2532T>C synonymous_variant 0.18 rifampicin
rpoB 762347 c.2541T>C synonymous_variant 0.15 rifampicin
rpoB 762353 c.2547C>T synonymous_variant 0.16 rifampicin
rpoB 762362 p.Glu852Asp missense_variant 0.14 rifampicin
rpoB 762369 c.2563T>C synonymous_variant 0.14 rifampicin
rpoC 762380 c.-990T>G upstream_gene_variant 0.13 rifampicin
rpoC 762410 c.-960T>A upstream_gene_variant 0.15 rifampicin
rpoB 762416 c.2610A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 762434 c.-936T>C upstream_gene_variant 0.16 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763034 c.3228C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763528 c.159G>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763603 c.234C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763621 c.252C>T synonymous_variant 0.14 rifampicin
rpoC 763633 c.264T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.16 rifampicin
rpoC 763657 c.288G>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763666 c.297G>T synonymous_variant 0.14 rifampicin
rpoC 763702 c.333C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763978 c.609C>G synonymous_variant 0.17 rifampicin
rpoC 763996 c.627T>C synonymous_variant 0.13 rifampicin
rpoC 764002 c.633C>G synonymous_variant 0.14 rifampicin
rpoC 764005 c.636G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764803 c.1434C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764817 p.Val483Gly missense_variant 0.88 rifampicin Uncertain significance
rpoC 765700 c.2331T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
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 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.21 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>T non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473202 n.1357C>T non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474638 n.981C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474711 n.1054G>A non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1474715 n.1058T>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474716 n.1059A>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474717 n.1060A>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1476033 n.2376T>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1476046 n.2389G>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476108 n.2451T>C non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1476583 n.2926G>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476628 n.2971T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
fabG1 1673338 c.-102G>A upstream_gene_variant 0.99 ethionamide
isoniazid
tsnR 1853565 c.-41G>A upstream_gene_variant 0.99 linezolid Uncertain significance
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
bacA 2062922 p.Ile603Val missense_variant 1.0 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2101921 c.1122G>A synonymous_variant 0.99 ethionamide Not assoc w R - Interim
delamanid Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ndh 2103112 c.-70G>T upstream_gene_variant 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
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 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2290062 c.-821G>A upstream_gene_variant 1.0 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
Rv2477c 2783914 c.129T>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783917 c.126C>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 1.0 cycloserine
Rv3083 3449324 p.Arg274Gln missense_variant 1.0 ethionamide Uncertain significance
whiB7 3568480 p.Gly67Val missense_variant 1.0 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
lpqB 3624162 p.Glu250Ala missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 0.98 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626969 c.-356C>G upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3626972 c.-359A>G upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3626996 c.-383G>A upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3627008 c.-395G>C upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3627011 c.-398T>G upstream_gene_variant 0.14 bedaquiline
rifampicin
alr 3840932 c.489C>T synonymous_variant 1.0 cycloserine
rpoA 3877764 c.744C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877848 c.660C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878061 c.447G>C synonymous_variant 0.13 rifampicin
rpoA 3878067 c.441C>G synonymous_variant 0.13 rifampicin
rpoA 3878103 c.405A>G synonymous_variant 0.14 rifampicin
rpoA 3878106 c.402G>C synonymous_variant 0.15 rifampicin
rpoA 3878118 c.390T>C synonymous_variant 0.16 rifampicin
rpoA 3878130 c.378C>G synonymous_variant 0.15 rifampicin
rpoA 3878143 p.Gly122Asp missense_variant 0.15 rifampicin Uncertain significance
rpoA 3878163 c.345C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878184 c.324C>A synonymous_variant 0.2 rifampicin
rpoA 3878193 c.315T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878217 c.291A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878229 c.279C>G synonymous_variant 0.2 rifampicin
rpoA 3878232 c.276G>C synonymous_variant 0.19 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878283 p.Glu75Asp missense_variant 0.18 rifampicin Uncertain significance
rpoA 3878292 c.216T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878298 c.210A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3878304 c.204G>T synonymous_variant 0.2 rifampicin
rpoA 3878313 c.195G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878322 c.186A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878331 c.177A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878337 c.171T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878346 c.162T>C synonymous_variant 0.18 rifampicin
rpoA 3878358 c.150C>G synonymous_variant 0.19 rifampicin
rpoA 3878361 c.147G>T synonymous_variant 0.2 rifampicin
rpoA 3878364 c.144A>C synonymous_variant 0.19 rifampicin
rpoA 3878385 c.123C>G synonymous_variant 0.18 rifampicin
rpoA 3878391 c.117T>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878400 c.108T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878409 c.99C>G synonymous_variant 0.19 rifampicin
rpoA 3878436 c.72A>G synonymous_variant 0.14 rifampicin
ddn 3986987 c.144G>T synonymous_variant 1.0 delamanid Not assoc w R - Interim
pretomanid
ddn 3987180 p.Asp113Asn missense_variant 1.0 delamanid Uncertain significance
pretomanid
clpC1 4040824 c.-120C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4139131 p.Glu209Lys missense_variant 0.99 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Not assoc w R
isoniazid Uncertain significance
glpK 4139183 c.572dupG frameshift_variant 0.95 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
glpK 4139789 c.-34C>T upstream_gene_variant 1.0 ethambutol Uncertain significance
moxifloxacin
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4239843 c.-20A>C upstream_gene_variant 1.0 ethambutol Not assoc w R - Interim
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244220 c.988C>T synonymous_variant 0.99 ethambutol Not assoc w R
embA 4244635 p.Val468Ala missense_variant 1.0 ethambutol Not assoc w R - Interim
embA 4245147 p.Pro639Ser missense_variant 0.96 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.99 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326279 p.Ser399Pro missense_variant 0.99 ethionamide Uncertain significance
ethA 4327103 p.Gly124Asp missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.99 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R