TB-Profiler result

Run: 38842841-a06f-418e-ae93-baf6dd357a98
Summary

Run ID: 38842841-a06f-418e-ae93-baf6dd357a98

Sample name:

Date: 29-01-2024 00:17:16

Number of reads: 634161

Percentage reads mapped: 96.17

Median coverage: 17

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG c.1484delG Uncertain significance
p.Thr12Pro Uncertain significance
ethambutol embB p.Ala313Val Uncertain significance
pyrazinamide
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin
amikacin
kanamycin
capreomycin
clofazimine
ethionamide ethA p.Gln271* 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
katG 2154627 c.1484delG frameshift_variant 0.12 isoniazid Uncertain significance
katG 2156078 p.Thr12Pro missense_variant 0.12 isoniazid Uncertain significance
embB 4247451 p.Ala313Val missense_variant 0.17 ethambutol Uncertain significance
ethA 4326663 p.Gln271* stop_gained 0.15 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 5078 c.-162C>A upstream_gene_variant 0.13 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 5108 c.-132G>T upstream_gene_variant 0.14 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 5675 p.Trp146Arg missense_variant 0.14 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 6036 p.Arg266His missense_variant 0.11 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 6157 c.918C>T synonymous_variant 0.1 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 6934 p.Gln565His missense_variant 0.19 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 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 8105 c.804G>T synonymous_variant 0.14 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 8957 p.Asp552Glu missense_variant 0.12 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9197 c.1901dupA frameshift_variant 0.12 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9280 p.Val660Gly missense_variant 0.15 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9611 c.2310C>T synonymous_variant 0.13 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9704 c.2403T>G synonymous_variant 0.14 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9709 p.Leu803Trp missense_variant 0.14 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
fgd1 490826 p.Phe15Cys missense_variant 0.12 delamanid
fgd1 491014 p.Thr78Pro missense_variant 0.18 delamanid
fgd1 491742 c.960T>C synonymous_variant 1.0 delamanid
mshA 575771 p.Val142Ile missense_variant 0.13 ethionamide
isoniazid
ccsA 619902 c.12G>T synonymous_variant 0.14 capreomycin
amikacin
ccsA 620091 p.Gln67His missense_variant 0.14 capreomycin
amikacin
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
ccsA 620650 p.Ala254Thr missense_variant 0.12 capreomycin
amikacin
ccsA 620679 c.789C>A synonymous_variant 0.11 capreomycin
amikacin
rpoB 760113 p.Asp103Asn missense_variant 0.12 rifampicin
rpoB 760124 c.319delG frameshift_variant 0.12 rifampicin
rpoB 760917 p.Arg371Cys missense_variant 0.18 rifampicin
rpoB 762176 c.2370T>G synonymous_variant 0.12 rifampicin
rpoB 762745 p.Gln980Leu missense_variant 1.0 rifampicin
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
rpoC 763700 p.Pro111Thr missense_variant 0.15 rifampicin
rpoC 764526 p.Arg386His missense_variant 0.2 rifampicin
rpoC 764676 p.Leu436Pro missense_variant 0.12 rifampicin
rpoC 764873 p.Pro502Thr missense_variant 0.15 rifampicin
rpoC 765705 p.Lys779Thr missense_variant 0.12 rifampicin
rpoC 765782 p.Ser805Ala missense_variant 0.12 rifampicin
rpoC 765791 p.Thr808Pro missense_variant 0.13 rifampicin
rpoC 765798 p.Asn810Thr missense_variant 0.12 rifampicin
rpoC 766100 p.Ile911Leu missense_variant 0.11 rifampicin
rpoC 766471 c.3102G>A synonymous_variant 0.13 rifampicin
rpoC 766621 p.Gln1084His missense_variant 0.13 rifampicin
rpoC 766911 p.Ile1181Ser missense_variant 0.17 rifampicin
rpoC 766945 c.3576A>C synonymous_variant 0.12 rifampicin
rpoC 767106 p.Asn1246Thr missense_variant 0.11 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776324 c.2157C>A synonymous_variant 0.11 clofazimine
bedaquiline
mmpL5 776485 p.Met666Leu missense_variant 0.11 clofazimine
bedaquiline
mmpL5 776495 c.1986G>A synonymous_variant 0.13 clofazimine
bedaquiline
mmpL5 776551 p.Thr644Ser missense_variant 0.11 clofazimine
bedaquiline
mmpL5 777123 p.Asp453Ala missense_variant 0.11 clofazimine
bedaquiline
mmpL5 777410 c.1071A>T synonymous_variant 0.13 clofazimine
bedaquiline
mmpL5 777555 p.Val309Asp missense_variant 0.12 clofazimine
bedaquiline
mmpL5 777759 p.Leu241Arg missense_variant 0.27 clofazimine
bedaquiline
mmpL5 778305 p.Ile59Arg missense_variant 0.17 clofazimine
bedaquiline
mmpR5 779263 p.Tyr92Asp missense_variant 0.11 clofazimine
bedaquiline
mmpR5 779401 p.Glu138* stop_gained 0.13 clofazimine
bedaquiline
mmpR5 779429 p.Glu147Val missense_variant 0.11 clofazimine
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rpsL 781557 c.-3T>A upstream_gene_variant 0.2 streptomycin
rpsL 781789 p.His77Pro missense_variant 0.1 streptomycin
rpsL 781872 p.Gln105Lys missense_variant 0.12 streptomycin
rpsL 781893 p.Gln112Lys missense_variant 0.12 streptomycin
rplC 800940 c.132C>T synonymous_variant 0.12 linezolid
rplC 801119 p.Glu104Ala missense_variant 0.11 linezolid
fbiC 1303233 p.Asn101Lys missense_variant 0.1 delamanid
fbiC 1303401 p.Gln157His missense_variant 0.14 delamanid
fbiC 1303995 c.1065C>T synonymous_variant 0.13 delamanid
Rv1258c 1406568 p.Val258Ala missense_variant 0.1 streptomycin
pyrazinamide
isoniazid
Rv1258c 1406665 p.Arg226Cys missense_variant 0.17 streptomycin
pyrazinamide
isoniazid
Rv1258c 1406718 p.Leu208Trp missense_variant 0.12 streptomycin
pyrazinamide
isoniazid
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1406824 p.Thr173Pro missense_variant 0.15 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1406867 c.474G>A synonymous_variant 0.11 streptomycin
pyrazinamide
isoniazid
Rv1258c 1407170 c.171C>T synonymous_variant 0.15 streptomycin
pyrazinamide
isoniazid
embR 1416518 p.Leu277Arg missense_variant 0.15 ethambutol
embR 1416621 p.Pro243Thr missense_variant 0.12 ethambutol
embR 1417020 p.Cys110Gly missense_variant 0.12 ethambutol
embR 1417124 p.Tyr75Ser missense_variant 0.15 ethambutol
embR 1417177 c.171C>T synonymous_variant 0.12 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrs 1471969 n.124T>C non_coding_transcript_exon_variant 0.2 linezolid
kanamycin
capreomycin
amikacin Uncertain significance
aminoglycosides
streptomycin
rrs 1472448 n.603T>C non_coding_transcript_exon_variant 0.13 linezolid
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
aminoglycosides
streptomycin Uncertain significance
rrl 1473667 n.10T>G non_coding_transcript_exon_variant 0.12 linezolid
rrl 1474649 n.992A>C non_coding_transcript_exon_variant 0.14 linezolid
rrl 1474677 n.1020A>C non_coding_transcript_exon_variant 0.17 linezolid
fabG1 1673558 p.His40Pro missense_variant 0.13 ethionamide
isoniazid
inhA 1673940 c.-262C>T upstream_gene_variant 0.15 ethionamide
isoniazid
inhA 1673955 c.-247G>T upstream_gene_variant 0.15 ethionamide
isoniazid
inhA 1674036 c.-166G>A upstream_gene_variant 0.13 ethionamide
isoniazid
inhA 1674963 c.762G>T synonymous_variant 0.18 ethionamide
isoniazid
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide
rpsA 1834921 c.1380G>A synonymous_variant 0.17 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 0.92 capreomycin
ndh 2102037 p.Ala336Ser missense_variant 0.1 ethionamide
isoniazid
ndh 2102096 p.Asn316Ser missense_variant 0.11 ethionamide
isoniazid
katG 2154676 p.Ala479Val missense_variant 0.11 isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Uncertain significance
katG 2155654 p.Lys153Thr missense_variant 0.13 isoniazid
katG 2155661 p.Val151Ile missense_variant 0.15 isoniazid
PPE35 2167802 c.2811T>G synonymous_variant 0.11 pyrazinamide
PPE35 2167895 p.Asn906Lys missense_variant 0.11 pyrazinamide
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169561 p.Leu351Arg missense_variant 0.14 pyrazinamide
PPE35 2170001 c.612C>A synonymous_variant 0.13 pyrazinamide
PPE35 2170268 c.345C>A synonymous_variant 0.11 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2289612 c.-371A>C upstream_gene_variant 0.13 pyrazinamide
pncA 2289613 c.-372T>G upstream_gene_variant 0.14 pyrazinamide
pncA 2289891 c.-650G>T upstream_gene_variant 0.11 pyrazinamide
kasA 2518113 c.-2A>C upstream_gene_variant 0.14 isoniazid
kasA 2518235 p.Ser41Gly missense_variant 0.15 isoniazid
kasA 2519066 p.Gly318Arg missense_variant 0.2 isoniazid
eis 2714391 c.942T>G synonymous_variant 0.15 kanamycin
amikacin
eis 2714406 c.927T>G synonymous_variant 0.18 kanamycin
amikacin
eis 2714432 p.Val301Ile missense_variant 0.25 kanamycin Uncertain significance
amikacin Uncertain significance
folC 2747216 p.Glu128Ala missense_variant 0.11 para-aminosalicylic_acid
folC 2747789 c.-191G>C upstream_gene_variant 0.15 para-aminosalicylic_acid
pepQ 2860609 c.-191A>C upstream_gene_variant 0.1 clofazimine
bedaquiline
ribD 2986938 p.Tyr34Asp missense_variant 0.12 para-aminosalicylic_acid
Rv2752c 3064748 p.Gly482Ser missense_variant 0.11 rifampicin
isoniazid
Rv2752c 3064890 c.1302C>A synonymous_variant 0.13 rifampicin
isoniazid
Rv2752c 3065129 c.1063C>T synonymous_variant 1.0 rifampicin
isoniazid
Rv2752c 3065135 p.Asp353Asn missense_variant 0.17 rifampicin
isoniazid
Rv2752c 3065401 p.Arg264Gln missense_variant 0.12 rifampicin
isoniazid
Rv2752c 3065523 c.669C>T synonymous_variant 0.1 rifampicin
isoniazid
Rv2752c 3066176 p.Pro6Ala missense_variant 0.15 rifampicin
isoniazid
Rv2752c 3067055 c.-864A>C upstream_gene_variant 0.15 rifampicin
isoniazid
Rv2752c 3067138 c.-947T>G upstream_gene_variant 0.15 rifampicin
isoniazid
thyA 3074101 p.Asp124Ala missense_variant 0.13 para-aminosalicylic_acid
thyA 3074310 c.162G>A synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3074366 p.Tyr36His missense_variant 0.1 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3086799 c.-21A>C upstream_gene_variant 0.12 cycloserine
ald 3087435 p.Gln206* stop_gained 0.15 cycloserine
Rv3083 3448326 c.-178T>C upstream_gene_variant 0.13 ethionamide
Rv3083 3448940 p.Asp146Gly missense_variant 0.11 ethionamide
Rv3083 3449358 p.Asn285Lys missense_variant 0.12 ethionamide
Rv3083 3449639 p.Glu379Gly missense_variant 0.17 ethionamide
Rv3083 3449848 p.Asp449Asn missense_variant 0.11 ethionamide
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
fprA 3474896 p.Asp297Val missense_variant 0.2 capreomycin
amikacin
fprA 3474993 c.987G>A synonymous_variant 1.0 capreomycin
amikacin
whiB7 3568535 p.Arg49Gly missense_variant 0.11 streptomycin
kanamycin
amikacin
whiB7 3568596 p.Trp28Cys missense_variant 0.14 streptomycin
kanamycin
amikacin
whiB7 3568600 p.Leu27Arg missense_variant 0.1 streptomycin
kanamycin
amikacin
whiB7 3568793 c.-114C>A upstream_gene_variant 0.15 streptomycin
kanamycin
amikacin
Rv3236c 3612335 p.Met261Arg missense_variant 0.12 pyrazinamide
Rv3236c 3612444 p.Ile225Leu missense_variant 0.15 pyrazinamide
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Uncertain significance
Rv3236c 3612829 p.Asp96Glu missense_variant 0.17 pyrazinamide
Rv3236c 3613149 c.-33G>A upstream_gene_variant 0.12 pyrazinamide
Rv3236c 3613155 c.-39T>G upstream_gene_variant 0.14 pyrazinamide
fbiA 3640355 c.-188C>T upstream_gene_variant 0.12 delamanid
fbiA 3640367 c.-176A>G upstream_gene_variant 0.13 delamanid
fbiA 3641257 p.Pro239Thr missense_variant 0.13 delamanid
fbiA 3641404 p.Trp288Gly missense_variant 0.17 delamanid
fbiA 3641473 p.Thr311Pro missense_variant 0.11 delamanid
fbiB 3642080 c.546A>C synonymous_variant 0.14 delamanid
fbiB 3642093 p.Leu187Val missense_variant 0.13 delamanid
fbiB 3642281 c.747C>A synonymous_variant 0.15 delamanid
fbiB 3642498 p.Thr322Pro missense_variant 0.17 delamanid
alr 3840385 p.Phe346Val missense_variant 0.13 cycloserine
alr 3840808 p.Asp205Asn missense_variant 0.12 cycloserine
rpoA 3877858 p.Glu217Ala missense_variant 0.13 rifampicin
rpoA 3878081 p.Gly143Cys missense_variant 0.18 rifampicin
rpoA 3878412 p.Tyr32* stop_gained 0.1 rifampicin
rpoA 3878424 c.84G>A synonymous_variant 0.14 rifampicin
clpC1 4038438 p.Lys756Met missense_variant 0.15 pyrazinamide
clpC1 4040230 p.Gly159Arg missense_variant 0.17 pyrazinamide Uncertain significance
clpC1 4040365 p.Arg114* stop_gained 0.15 pyrazinamide
panD 4044345 c.-64C>T upstream_gene_variant 0.11 pyrazinamide
embC 4239773 c.-90A>C upstream_gene_variant 0.1 ethambutol
embC 4240931 p.Trp357Gly missense_variant 0.18 ethambutol
embC 4241352 p.Ile497Ser missense_variant 0.14 ethambutol
embC 4242096 p.Ala745Val missense_variant 0.12 ethambutol
embC 4242239 p.Asp793Tyr missense_variant 0.12 ethambutol
embA 4242974 c.-259C>T upstream_gene_variant 0.17 ethambutol
embA 4243185 c.-48G>T upstream_gene_variant 0.13 ethambutol
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol
embA 4243800 p.Asp190Tyr missense_variant 0.13 ethambutol
embA 4243954 p.Arg241His missense_variant 0.14 ethambutol Uncertain significance
embA 4244933 c.1701A>C synonymous_variant 0.18 ethambutol
embA 4245494 c.2262G>A synonymous_variant 1.0 ethambutol
embB 4245623 c.-891G>T upstream_gene_variant 0.13 ethambutol
embB 4247317 c.804G>T synonymous_variant 0.12 ethambutol
embB 4248020 p.Leu503Val missense_variant 0.12 ethambutol
embB 4248558 p.Tyr682Ser missense_variant 0.11 ethambutol
aftB 4267070 c.1767C>A synonymous_variant 0.18 capreomycin
amikacin
aftB 4267086 p.Leu584Arg missense_variant 0.17 capreomycin
amikacin
aftB 4267433 c.1404C>T synonymous_variant 0.11 capreomycin
amikacin
aftB 4267647 p.Asp397Gly missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
aftB 4268853 c.-17T>G upstream_gene_variant 0.1 capreomycin
amikacin
aftB 4268865 c.-29T>G upstream_gene_variant 0.11 capreomycin
amikacin
aftB 4268921 c.-85C>T upstream_gene_variant 0.12 capreomycin
amikacin
ubiA 4269440 p.Leu132Ile missense_variant 0.18 ethambutol
ubiA 4270020 c.-187C>A upstream_gene_variant 0.13 ethambutol
ethA 4326676 p.Ser266Arg missense_variant 1.0 ethionamide Uncertain significance
ethR 4326832 c.-717C>A upstream_gene_variant 0.15 ethionamide
ethR 4327264 c.-285G>C upstream_gene_variant 0.11 ethionamide
ethA 4327806 c.-333G>T upstream_gene_variant 0.12 ethionamide
whiB6 4338266 p.Arg86Trp missense_variant 0.13 streptomycin
capreomycin
amikacin
whiB6 4338499 p.Glu8Gly missense_variant 0.12 streptomycin Uncertain significance
capreomycin
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407530 c.673T>G stop_lost&splice_region_variant 0.15 streptomycin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin
gid 4407789 c.414G>T synonymous_variant 0.11 streptomycin
gid 4408149 c.54T>G synonymous_variant 0.11 streptomycin
gid 4408368 c.-166A>G upstream_gene_variant 0.11 streptomycin