TB-Profiler result

Run: a1212940-5210-41bb-8f3c-0c47346f0e49
Summary

Run ID: a1212940-5210-41bb-8f3c-0c47346f0e49

Sample name:

Date: 29-03-2024 07:16:05

Number of reads: 16119839

Percentage reads mapped: 90.77

Median coverage: 274

Strain: lineage1.2.2.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1 Indo-Oceanic RD239 0.98
lineage1.2.2 Indo-Oceanic RD239 1.0
lineage1.2.2.2 Indo-Oceanic RD239 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.His445Asn Assoc w R
isoniazid inhA p.Ser94Ala Uncertain significance
ethambutol
pyrazinamide
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin rrs n.514A>T Uncertain significance
amikacin
kanamycin
capreomycin
clofazimine
ethionamide inhA p.Ser94Ala Assoc w R - interim
para-aminosalicylic_acid
cycloserine
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 761139 p.His445Asn missense_variant 1.0 rifampicin Assoc w R
rrs 1472359 n.514A>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance
inhA 1674481 p.Ser94Ala missense_variant 0.99 isoniazid Uncertain significance
ethionamide Assoc w R - interim
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 5075 c.-165C>T upstream_gene_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrB 6112 p.Met291Ile missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 6634 c.-668T>G upstream_gene_variant 0.13 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 6934 p.Gln565His missense_variant 0.19 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7268 c.-34C>T upstream_gene_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7362 p.Glu21Gln missense_variant 0.99 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 8445 p.Arg382Gly missense_variant 0.14 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8452 p.Ala384Val missense_variant 0.98 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9143 c.1842T>C synonymous_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 0.99 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9585 p.Leu762Val missense_variant 0.14 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
fgd1 490696 c.-87T>G upstream_gene_variant 0.23 delamanid
fgd1 490751 c.-32T>G upstream_gene_variant 0.11 delamanid
fgd1 491014 p.Thr78Pro missense_variant 0.12 delamanid
fgd1 491316 c.534C>G synonymous_variant 0.27 delamanid
fgd1 491324 p.Val181Gly missense_variant 0.12 delamanid
fgd1 491742 c.960T>C synonymous_variant 1.0 delamanid
mshA 575308 c.-40A>G upstream_gene_variant 0.14 ethionamide
isoniazid
mshA 575309 c.-39C>G upstream_gene_variant 0.12 ethionamide
isoniazid
mshA 575356 c.9T>G synonymous_variant 0.11 ethionamide
isoniazid
mshA 575428 c.81G>C synonymous_variant 0.15 ethionamide
isoniazid
mshA 575964 p.Val206Gly missense_variant 0.12 ethionamide
isoniazid
mshA 576780 p.Val478Gly missense_variant 0.14 ethionamide
isoniazid
ccsA 619831 c.-60T>G upstream_gene_variant 0.15 capreomycin
amikacin
ccsA 620053 p.Ala55Arg missense_variant 0.11 capreomycin
amikacin
rpoB 759620 c.-187A>C upstream_gene_variant 0.13 rifampicin
rpoB 761305 p.Val500Gly missense_variant 0.12 rifampicin
rpoB 762625 p.Val940Gly missense_variant 0.12 rifampicin
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
rpoC 763552 c.183C>T synonymous_variant 1.0 rifampicin
rpoC 763884 p.Ala172Val missense_variant 0.99 rifampicin Uncertain significance
rpoC 763886 c.517C>A synonymous_variant 1.0 rifampicin
rpoC 764328 p.Ile320Thr missense_variant 0.12 rifampicin
rpoC 764751 p.Val461Gly missense_variant 0.19 rifampicin
rpoC 765300 p.Val644Gly missense_variant 0.12 rifampicin
rpoC 766938 p.Asn1190Thr missense_variant 0.11 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776098 p.Thr795Pro missense_variant 0.12 clofazimine
bedaquiline
mmpL5 776100 p.Thr794Ile missense_variant 0.93 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776263 p.Thr740Pro missense_variant 0.14 clofazimine
bedaquiline
mmpL5 777336 p.Val382Gly missense_variant 0.11 clofazimine
bedaquiline
mmpL5 777354 p.Val376Gly missense_variant 0.21 clofazimine
bedaquiline
mmpL5 777502 p.Thr327Pro missense_variant 0.16 clofazimine
bedaquiline
mmpS5 778569 p.Thr113Pro missense_variant 0.15 clofazimine
bedaquiline
mmpS5 779625 c.-720G>A upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 0.99 streptomycin Uncertain significance
rpsL 781877 c.318T>G synonymous_variant 0.12 streptomycin
rplC 801156 c.348T>G synonymous_variant 0.12 linezolid
fbiC 1303640 p.Asp237Ala missense_variant 0.14 delamanid
Rv1258c 1406358 p.Ile328Thr missense_variant 0.19 streptomycin
pyrazinamide
isoniazid
Rv1258c 1406363 c.978A>C synonymous_variant 0.12 streptomycin
pyrazinamide
isoniazid
Rv1258c 1407513 c.-173T>G upstream_gene_variant 0.15 streptomycin
pyrazinamide
isoniazid
Rv1258c 1407522 c.-182C>G upstream_gene_variant 0.14 streptomycin
pyrazinamide
isoniazid
embR 1416448 c.900C>T synonymous_variant 0.12 ethambutol
embR 1416746 p.His201Pro missense_variant 0.12 ethambutol
embR 1417019 p.Cys110Tyr missense_variant 1.0 ethambutol Uncertain significance
embR 1417367 c.-20C>A upstream_gene_variant 0.14 ethambutol
embR 1417501 c.-154A>C upstream_gene_variant 0.12 ethambutol
embR 1417513 c.-166A>C upstream_gene_variant 0.12 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1473360 n.1515T>G non_coding_transcript_exon_variant 0.14 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1474928 n.1271C>A non_coding_transcript_exon_variant 0.12 linezolid
rrl 1474935 n.1278A>C non_coding_transcript_exon_variant 0.14 linezolid
fabG1 1674076 p.Thr213Pro missense_variant 0.14 ethionamide
isoniazid
rpsA 1834631 p.Gln364Lys missense_variant 0.15 pyrazinamide
tlyA 1917817 c.-123A>C upstream_gene_variant 0.15 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
tlyA 1918225 p.Phe96Val missense_variant 0.12 capreomycin
tlyA 1918377 c.438T>G synonymous_variant 0.12 capreomycin
tlyA 1918626 c.687G>C synonymous_variant 0.16 capreomycin
ndh 2102240 p.Arg268His missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
ndh 2102539 c.504C>A synonymous_variant 0.12 ethionamide
isoniazid
katG 2154036 p.Ser692Arg missense_variant 0.17 isoniazid Uncertain significance
katG 2154627 c.1485T>G synonymous_variant 0.12 isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Uncertain significance
katG 2154793 p.Asp440Gly missense_variant 0.14 isoniazid
katG 2154992 p.Ser374Pro missense_variant 0.14 isoniazid
katG 2155375 p.Val246Gly missense_variant 0.13 isoniazid Uncertain significance
katG 2155774 p.Tyr113Ser missense_variant 0.12 isoniazid
katG 2155778 p.Thr112Pro missense_variant 0.15 isoniazid Uncertain significance
katG 2155817 p.Gly99Arg missense_variant 0.13 isoniazid Uncertain significance
katG 2156210 c.-99T>G upstream_gene_variant 0.11 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2168742 p.Gly624Asp missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169379 p.Phe412Val missense_variant 0.11 pyrazinamide
PPE35 2169986 p.Leu209Phe missense_variant 0.17 pyrazinamide
PPE35 2170104 p.Leu170Pro missense_variant 0.16 pyrazinamide
PPE35 2170131 p.Val161Gly missense_variant 0.22 pyrazinamide
PPE35 2170144 p.Gly157Arg missense_variant 0.13 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2222413 p.Asn251Thr missense_variant 0.11 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2290023 c.-782A>C upstream_gene_variant 0.23 pyrazinamide
pncA 2290027 c.-786G>C upstream_gene_variant 0.12 pyrazinamide
kasA 2518101 c.-14G>T upstream_gene_variant 0.12 isoniazid
kasA 2518132 c.18C>T synonymous_variant 0.97 isoniazid
kasA 2518891 c.777C>A synonymous_variant 0.19 isoniazid
kasA 2519332 c.1218C>G synonymous_variant 0.16 isoniazid
eis 2714312 p.Thr341Pro missense_variant 0.12 kanamycin
amikacin
eis 2714348 p.Phe329Val missense_variant 0.11 kanamycin
amikacin
eis 2714366 p.Val323Leu missense_variant 0.24 kanamycin
amikacin
eis 2714528 p.Thr269Pro missense_variant 0.14 kanamycin
amikacin
eis 2715019 p.His105Pro missense_variant 0.13 kanamycin
amikacin
eis 2715586 c.-254G>C upstream_gene_variant 0.25 kanamycin
amikacin
ahpC 2725954 c.-239C>T upstream_gene_variant 0.23 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.98 isoniazid
ahpC 2726255 c.63T>G synonymous_variant 0.13 isoniazid
ahpC 2726737 p.Asp182Ala missense_variant 0.23 isoniazid
folC 2746745 p.Val285Gly missense_variant 0.13 para-aminosalicylic_acid
pepQ 2859832 p.Ala196Gly missense_variant 0.14 clofazimine
bedaquiline
pepQ 2859931 p.Leu163Arg missense_variant 0.13 clofazimine
bedaquiline
pepQ 2859944 p.Ala159Pro missense_variant 0.2 clofazimine
bedaquiline
pepQ 2859949 p.Leu157Trp missense_variant 0.15 clofazimine
bedaquiline
ribD 2987281 p.Val148Gly missense_variant 0.11 para-aminosalicylic_acid
Rv2752c 3065978 p.Asp72Tyr missense_variant 0.15 rifampicin
isoniazid
thyX 3067246 p.Thr234Pro missense_variant 0.12 para-aminosalicylic_acid
thyX 3067786 p.Thr54Pro missense_variant 0.14 para-aminosalicylic_acid
thyX 3067965 c.-20C>G upstream_gene_variant 0.15 para-aminosalicylic_acid
thyA 3073817 p.Gln219Glu missense_variant 0.24 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339302 p.Ile62Thr missense_variant 0.13 delamanid
fbiD 3339304 p.Thr63Pro missense_variant 0.38 delamanid
Rv3083 3448353 c.-151T>G upstream_gene_variant 0.19 ethionamide
Rv3083 3448484 c.-20T>G upstream_gene_variant 0.11 ethionamide
Rv3083 3448714 p.Asp71His missense_variant 0.99 ethionamide Uncertain significance
Rv3083 3448897 p.Thr132Pro missense_variant 0.13 ethionamide
Rv3083 3449673 p.Tyr390* stop_gained 0.18 ethionamide
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
fprA 3474400 p.Tyr132Asp missense_variant 0.2 capreomycin
amikacin
fprA 3474597 c.591C>A synonymous_variant 1.0 capreomycin
amikacin
fprA 3474986 p.Val327Gly missense_variant 0.12 capreomycin
amikacin
fprA 3475044 c.1038C>G synonymous_variant 0.12 capreomycin
amikacin
fprA 3475159 p.Asn385Asp missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
fprA 3475280 p.Val425Gly missense_variant 0.19 capreomycin
amikacin
fprA 3475308 c.1302C>G synonymous_variant 0.12 capreomycin
amikacin
Rv3236c 3611982 p.Ala379Pro missense_variant 0.19 pyrazinamide
Rv3236c 3611992 c.1125T>G synonymous_variant 0.16 pyrazinamide
Rv3236c 3612425 p.Ala231Gly missense_variant 0.13 pyrazinamide
Rv3236c 3612835 c.282T>G synonymous_variant 0.18 pyrazinamide
Rv3236c 3612965 p.Val51Gly missense_variant 0.12 pyrazinamide
fbiA 3641063 p.Val174Gly missense_variant 0.12 delamanid
fbiB 3641847 p.Ala105Pro missense_variant 0.11 delamanid
fbiB 3642033 p.Ala167Pro missense_variant 0.13 delamanid
alr 3840494 c.927G>C synonymous_variant 0.15 cycloserine
rpoA 3877766 p.Ala248Pro missense_variant 0.13 rifampicin
rpoA 3878192 p.Thr106Pro missense_variant 0.14 rifampicin
rpoA 3878580 c.-73A>C upstream_gene_variant 0.15 rifampicin
rpoA 3878586 c.-79A>C upstream_gene_variant 0.12 rifampicin
ddn 3986749 c.-95C>G upstream_gene_variant 0.12 delamanid
ddn 3987025 p.Val61Gly missense_variant 0.23 delamanid
clpC1 4038328 p.Glu793Gln missense_variant 0.99 pyrazinamide Uncertain significance
clpC1 4039484 c.1221T>G synonymous_variant 0.11 pyrazinamide
clpC1 4039931 c.774T>G synonymous_variant 0.15 pyrazinamide
clpC1 4040225 c.480A>G synonymous_variant 0.15 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 1.0 pyrazinamide Uncertain significance
clpC1 4040719 c.-15A>G upstream_gene_variant 1.0 pyrazinamide Uncertain significance
clpC1 4040749 c.-45T>G upstream_gene_variant 0.11 pyrazinamide
clpC1 4040756 c.-52T>G upstream_gene_variant 0.19 pyrazinamide
panD 4044471 c.-190T>G upstream_gene_variant 0.17 pyrazinamide
embC 4239866 p.Ala2Pro missense_variant 0.13 ethambutol
embC 4239870 p.Thr3Asn missense_variant 0.13 ethambutol
embC 4240108 p.Leu82Phe missense_variant 0.11 ethambutol
embC 4240671 p.Thr270Ile missense_variant 0.99 ethambutol Uncertain significance
embC 4240841 p.Tyr327Asp missense_variant 0.13 ethambutol
embC 4241042 p.Asn394Asp missense_variant 1.0 ethambutol Uncertain significance
embC 4241429 p.Phe523Val missense_variant 0.15 ethambutol
embC 4241454 p.Ile531Thr missense_variant 0.14 ethambutol
embC 4241456 p.Ala532Pro missense_variant 0.19 ethambutol
embC 4241783 p.Trp641Gly missense_variant 0.15 ethambutol
embC 4242232 c.2370T>C synonymous_variant 0.16 ethambutol
embA 4242559 c.-674G>A upstream_gene_variant 1.0 ethambutol
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4244217 p.Thr329Pro missense_variant 0.12 ethambutol
embA 4245670 p.Ala813Gly missense_variant 0.99 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 1.0 ethambutol Uncertain significance
embB 4246316 c.-198T>G upstream_gene_variant 0.11 ethambutol
embB 4246979 p.Gly156Cys missense_variant 0.99 ethambutol Uncertain significance
embB 4247041 c.528C>T synonymous_variant 0.12 ethambutol
embB 4247603 p.Leu364Val missense_variant 0.15 ethambutol
embB 4247623 c.1110G>C synonymous_variant 0.13 ethambutol
embB 4247632 c.1119C>G synonymous_variant 0.14 ethambutol
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Uncertain significance
embB 4247656 p.Lys381Asn missense_variant 0.14 ethambutol
embB 4249403 p.Thr964Pro missense_variant 0.2 ethambutol
embB 4249504 p.Gln997His missense_variant 0.12 ethambutol
embB 4249664 p.Thr1051Pro missense_variant 0.14 ethambutol
aftB 4267156 p.Gln561Lys missense_variant 0.13 capreomycin
amikacin
aftB 4267542 p.Tyr432Ser missense_variant 0.12 capreomycin
amikacin
aftB 4267960 p.Val293Met missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
aftB 4268006 c.831A>G synonymous_variant 0.11 capreomycin
amikacin
ubiA 4269162 p.Leu224Phe missense_variant 0.99 ethambutol
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Uncertain significance
aftB 4269606 c.-770T>C upstream_gene_variant 1.0 capreomycin
amikacin
ethA 4326148 c.1326G>T synonymous_variant 0.99 ethionamide
ethA 4326439 p.Asn345Lys missense_variant 0.99 ethionamide Uncertain significance
ethR 4328041 p.Thr165Pro missense_variant 0.18 ethionamide
ethA 4328467 c.-994G>C upstream_gene_variant 0.13 ethionamide
whiB6 4338203 p.Arg107Cys missense_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin
gid 4407848 p.Ala119Thr missense_variant 0.99 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 1.0 streptomycin
gid 4408302 c.-100A>C upstream_gene_variant 0.17 streptomycin
gid 4408310 c.-108G>C upstream_gene_variant 0.13 streptomycin
gid 4408314 c.-112G>C upstream_gene_variant 0.14 streptomycin