TB-Profiler result

Run: b0855c23-4702-49e9-9f35-4f2fa9608f69
Summary

Run ID: b0855c23-4702-49e9-9f35-4f2fa9608f69

Sample name:

Date: 08-05-2024 05:08:03

Number of reads: 4939873

Percentage reads mapped: 96.55

Median coverage: 87

Strain: lineage4.8

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 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 inhA c.-154G>A Assoc w R
ethambutol
pyrazinamide
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin
amikacin
kanamycin
capreomycin
clofazimine
ethionamide inhA c.-154G>A 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
inhA 1674048 c.-154G>A upstream_gene_variant 1.0 isoniazid Assoc w R
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
gyrA 6922 c.-380G>T upstream_gene_variant 0.13 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 6934 p.Gln565His missense_variant 0.17 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 9647 c.2346C>G synonymous_variant 0.13 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9657 p.Thr786Pro missense_variant 0.11 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
fgd1 490696 c.-87T>G upstream_gene_variant 0.11 delamanid
fgd1 490751 c.-32T>G upstream_gene_variant 0.13 delamanid
fgd1 491014 p.Thr78Pro missense_variant 0.18 delamanid
fgd1 491324 p.Val181Gly missense_variant 0.25 delamanid
mshA 575298 c.-50T>G upstream_gene_variant 0.13 ethionamide
isoniazid
mshA 575308 c.-40A>G upstream_gene_variant 0.21 ethionamide
isoniazid
mshA 575955 p.Glu203Gly missense_variant 0.11 ethionamide
isoniazid
mshA 576618 p.His424Pro missense_variant 0.18 ethionamide
isoniazid
mshA 576723 p.Val459Gly missense_variant 0.12 ethionamide
isoniazid
mshA 576751 p.Lys468Asn missense_variant 0.16 ethionamide
isoniazid
ccsA 620748 c.858T>G synonymous_variant 0.14 capreomycin
amikacin
rpoB 759615 c.-192A>C upstream_gene_variant 0.12 rifampicin
rpoB 759620 c.-187A>C upstream_gene_variant 0.13 rifampicin
rpoB 759816 p.Ser4Pro missense_variant 0.12 rifampicin
rpoB 759831 p.Thr9Pro missense_variant 0.18 rifampicin
rpoB 761885 c.2079T>G synonymous_variant 0.15 rifampicin
rpoB 761890 p.Val695Gly missense_variant 0.14 rifampicin
rpoB 762831 p.Ser1009Gly missense_variant 0.19 rifampicin
rpoB 762924 p.Thr1040Pro missense_variant 0.12 rifampicin
rpoC 765244 c.1875T>G synonymous_variant 0.13 rifampicin
rpoC 765353 p.Trp662Gly missense_variant 0.11 rifampicin
rpoC 765381 p.Val671Gly missense_variant 0.13 rifampicin
rpoC 766585 c.3216T>G synonymous_variant 0.12 rifampicin
rpoC 766632 p.Val1088Gly missense_variant 0.25 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776098 p.Thr795Pro missense_variant 0.13 clofazimine
bedaquiline
mmpL5 777423 p.Leu353Arg missense_variant 0.12 clofazimine
bedaquiline
mmpL5 777427 p.Thr352Pro missense_variant 0.14 clofazimine
bedaquiline
mmpR5 779363 p.Leu125Arg missense_variant 0.12 clofazimine
bedaquiline
mmpR5 779369 p.Asp127Ala missense_variant 0.12 clofazimine
bedaquiline
mmpR5 779371 p.Ala128Pro missense_variant 0.16 clofazimine
bedaquiline
rpsL 781363 c.-197T>G upstream_gene_variant 0.25 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rplC 801287 p.Val160Gly missense_variant 0.15 linezolid
fbiC 1303016 p.Val29Gly missense_variant 0.2 delamanid
fbiC 1303649 p.Val240Gly missense_variant 0.15 delamanid
fbiC 1304096 p.Val389Gly missense_variant 0.12 delamanid
fbiC 1304270 p.Val447Gly missense_variant 0.12 delamanid
fbiC 1304485 p.Thr519Pro missense_variant 0.15 delamanid
Rv1258c 1406452 p.Thr297Pro missense_variant 0.17 streptomycin
pyrazinamide
isoniazid
Rv1258c 1407513 c.-173T>G upstream_gene_variant 0.15 streptomycin
pyrazinamide
isoniazid
atpE 1461083 c.39T>G synonymous_variant 0.12 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 linezolid Uncertain significance
rrl 1474369 n.712A>C non_coding_transcript_exon_variant 0.12 linezolid
rrl 1475019 n.1362T>G non_coding_transcript_exon_variant 0.17 linezolid
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.21 linezolid
fabG1 1673443 p.Thr2Pro missense_variant 0.12 ethionamide
isoniazid
fabG1 1673449 p.Thr4Pro missense_variant 0.13 ethionamide
isoniazid
fabG1 1673543 p.Leu35Arg missense_variant 0.15 ethionamide
isoniazid
inhA 1674816 c.615T>G synonymous_variant 0.15 ethionamide
isoniazid
inhA 1674827 p.Glu209Gly missense_variant 0.15 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674892 p.Asn231Asp missense_variant 0.15 ethionamide
isoniazid
inhA 1674926 p.Val242Gly missense_variant 0.19 ethionamide
isoniazid
rpsA 1834231 c.690T>G synonymous_variant 0.13 pyrazinamide
rpsA 1834236 p.Asp232Gly missense_variant 0.12 pyrazinamide
rpsA 1834240 c.699T>G synonymous_variant 0.15 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
tlyA 1918034 p.Val32Gly missense_variant 0.13 capreomycin
tlyA 1918069 p.Thr44Pro missense_variant 0.12 capreomycin
tlyA 1918265 p.Val109Gly missense_variant 0.11 capreomycin
ndh 2102897 p.His49Pro missense_variant 0.14 ethionamide
isoniazid
katG 2154487 p.Asp542Ala missense_variant 0.14 isoniazid
katG 2155660 p.Val151Gly missense_variant 0.21 isoniazid
katG 2155778 p.Thr112Pro missense_variant 0.17 isoniazid Uncertain significance
katG 2155798 p.Met105Arg missense_variant 0.13 isoniazid
katG 2155853 p.Ser87Pro missense_variant 0.12 isoniazid
katG 2155856 p.Thr86Pro missense_variant 0.11 isoniazid
PPE35 2167859 c.2754T>G synonymous_variant 0.13 pyrazinamide
PPE35 2168149 p.Pro822Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169317 c.1296C>T synonymous_variant 0.22 pyrazinamide
PPE35 2169320 p.Leu431Phe missense_variant 0.24 pyrazinamide
PPE35 2169379 p.Phe412Val missense_variant 0.12 pyrazinamide
PPE35 2169854 c.759T>G synonymous_variant 0.15 pyrazinamide
PPE35 2169862 p.Asn251His missense_variant 0.29 pyrazinamide
PPE35 2169866 c.747G>C synonymous_variant 0.17 pyrazinamide
PPE35 2170045 p.Thr190Pro missense_variant 0.12 pyrazinamide
PPE35 2170074 c.538dupG frameshift_variant 0.2 pyrazinamide
PPE35 2170082 c.531T>G synonymous_variant 0.29 pyrazinamide
PPE35 2170223 c.390T>C synonymous_variant 0.2 pyrazinamide
PPE35 2170227 p.Asn129Thr missense_variant 0.18 pyrazinamide
PPE35 2170455 p.Val53Gly missense_variant 0.11 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2289511 c.-270T>G upstream_gene_variant 0.12 pyrazinamide
pncA 2289900 c.-659A>C upstream_gene_variant 0.14 pyrazinamide
eis 2714366 p.Val323Leu missense_variant 0.23 kanamycin
amikacin
eis 2714569 p.Ala255Gly missense_variant 0.15 kanamycin
amikacin
eis 2715098 p.Thr79Pro missense_variant 0.15 kanamycin
amikacin
eis 2715103 p.Leu77Pro missense_variant 0.15 kanamycin Uncertain significance
amikacin Uncertain significance
ahpC 2725963 c.-230G>C upstream_gene_variant 0.11 isoniazid
ahpC 2726338 p.Val49Gly missense_variant 0.4 isoniazid
ahpC 2726341 p.Val50Gly missense_variant 0.28 isoniazid
ahpC 2726345 c.153C>T synonymous_variant 0.11 isoniazid
ahpC 2726350 p.Trp53Leu missense_variant 0.17 isoniazid
ahpC 2726756 c.564C>G synonymous_variant 0.14 isoniazid
ahpC 2726773 p.Ser194Leu missense_variant 0.13 isoniazid
pepQ 2859367 p.Met351Lys missense_variant 0.14 clofazimine
bedaquiline
pepQ 2859377 p.Thr348Ala missense_variant 0.29 clofazimine
bedaquiline
pepQ 2859381 c.1038C>G synonymous_variant 0.19 clofazimine
bedaquiline
pepQ 2859787 p.Val211Gly missense_variant 0.12 clofazimine
bedaquiline
ribD 2986648 c.-191T>G upstream_gene_variant 0.21 para-aminosalicylic_acid
ribD 2986652 c.-187T>G upstream_gene_variant 0.12 para-aminosalicylic_acid
ribD 2987268 p.Thr144Pro missense_variant 0.12 para-aminosalicylic_acid
ribD 2987271 p.Thr145Pro missense_variant 0.12 para-aminosalicylic_acid
ribD 2987296 p.Arg153Pro missense_variant 0.11 para-aminosalicylic_acid
ribD 2987396 c.558T>G synonymous_variant 0.24 para-aminosalicylic_acid
ribD 2987406 p.Ile190Val missense_variant 0.12 para-aminosalicylic_acid
Rv2752c 3064745 p.Thr483Pro missense_variant 0.24 rifampicin
isoniazid
thyX 3067953 c.-8T>G upstream_gene_variant 0.12 para-aminosalicylic_acid
thyX 3068024 c.-79A>C upstream_gene_variant 0.13 para-aminosalicylic_acid
thyX 3068031 c.-86A>C upstream_gene_variant 0.16 para-aminosalicylic_acid
thyX 3068042 c.-97T>C upstream_gene_variant 0.11 para-aminosalicylic_acid
thyA 3074645 c.-174T>G upstream_gene_variant 0.15 para-aminosalicylic_acid
ald 3087845 c.1026T>G synonymous_variant 0.13 cycloserine
fbiD 3339153 p.Leu12Phe missense_variant 0.19 delamanid
fbiD 3339168 c.51G>A synonymous_variant 0.12 delamanid
fbiD 3339174 p.Leu19Phe missense_variant 0.17 delamanid
fbiD 3339259 p.Thr48Pro missense_variant 0.14 delamanid
fbiD 3339273 c.156T>G synonymous_variant 0.14 delamanid
fbiD 3339304 p.Thr63Pro missense_variant 0.3 delamanid
fbiD 3339583 p.Thr156Pro missense_variant 0.2 delamanid
fbiD 3339593 p.His159Pro missense_variant 0.24 delamanid
fprA 3474919 p.Lys305Gln missense_variant 0.11 capreomycin
amikacin
fprA 3474977 p.Tyr324Ser missense_variant 0.11 capreomycin
amikacin
fprA 3475059 p.Ser351Arg missense_variant 0.11 capreomycin
amikacin
fprA 3475081 p.Trp359Gly missense_variant 0.21 capreomycin
amikacin
fprA 3475084 p.Ile360Val missense_variant 0.11 capreomycin
amikacin
Rv3236c 3611992 c.1125T>G synonymous_variant 0.19 pyrazinamide
Rv3236c 3611995 c.1122C>G synonymous_variant 0.11 pyrazinamide
fbiB 3641955 p.Gly141Arg missense_variant 0.15 delamanid
fbiB 3642531 p.Arg333Ser missense_variant 0.16 delamanid
fbiB 3642538 p.Val335Gly missense_variant 0.16 delamanid
fbiB 3642734 c.1200G>C synonymous_variant 0.12 delamanid
fbiB 3642744 p.Ala404Ser missense_variant 0.2 delamanid
fbiB 3642749 c.1215T>C synonymous_variant 0.11 delamanid
fbiB 3642754 p.Leu407Pro missense_variant 0.13 delamanid
alr 3840268 p.Thr385Pro missense_variant 0.17 cycloserine
rpoA 3878603 c.-96G>C upstream_gene_variant 0.18 rifampicin
rpoA 3878609 c.-102T>C upstream_gene_variant 0.18 rifampicin
rpoA 3878613 c.-106A>C upstream_gene_variant 0.18 rifampicin
rpoA 3878618 c.-111A>C upstream_gene_variant 0.17 rifampicin
rpoA 3878627 c.-120T>G upstream_gene_variant 0.15 rifampicin
rpoA 3878641 c.-134C>G upstream_gene_variant 0.16 rifampicin
ddn 3986997 p.Thr52Pro missense_variant 0.15 delamanid
ddn 3987025 p.Val61Gly missense_variant 0.16 delamanid
clpC1 4038857 c.1848C>A synonymous_variant 0.2 pyrazinamide
clpC1 4039484 c.1221T>G synonymous_variant 0.13 pyrazinamide
clpC1 4039834 p.Thr291Pro missense_variant 0.12 pyrazinamide
clpC1 4039932 p.Gly258Val missense_variant 0.24 pyrazinamide
clpC1 4039941 p.Leu255Arg missense_variant 0.12 pyrazinamide
clpC1 4040242 p.Thr155Pro missense_variant 0.14 pyrazinamide
panD 4044471 c.-190T>G upstream_gene_variant 0.13 pyrazinamide
embC 4239973 c.111T>G synonymous_variant 0.14 ethambutol
embC 4240408 c.546A>C synonymous_variant 0.13 ethambutol
embC 4240443 p.Arg194Pro missense_variant 0.17 ethambutol
embC 4240447 c.585G>C synonymous_variant 0.12 ethambutol
embC 4241454 p.Ile531Thr missense_variant 0.12 ethambutol
embC 4242450 p.Met863Arg missense_variant 0.11 ethambutol
embC 4242453 p.Leu864Arg missense_variant 0.11 ethambutol
embA 4242526 c.-707C>G upstream_gene_variant 0.13 ethambutol
embC 4242554 p.Leu898Val missense_variant 0.14 ethambutol
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embC 4242822 p.Val987Gly missense_variant 0.24 ethambutol
embC 4242827 p.Leu989Val missense_variant 0.11 ethambutol
embA 4243350 p.Thr40Pro missense_variant 0.21 ethambutol
embA 4243372 p.Gln47Arg missense_variant 0.15 ethambutol
embA 4243380 p.Thr50Pro missense_variant 0.13 ethambutol
embA 4243697 c.465A>C synonymous_variant 0.12 ethambutol
embA 4243963 p.Val244Gly missense_variant 0.18 ethambutol
embA 4244283 p.Pro351Ala missense_variant 0.11 ethambutol
embA 4244619 p.Leu463Val missense_variant 0.14 ethambutol
embA 4245927 p.Thr899Pro missense_variant 0.19 ethambutol
embA 4246423 p.Val1064Gly missense_variant 0.14 ethambutol
embB 4247076 p.Val188Gly missense_variant 0.14 ethambutol
embB 4248663 p.Val717Gly missense_variant 0.19 ethambutol
embB 4248757 c.2244A>G synonymous_variant 0.11 ethambutol
embB 4249401 p.Val963Gly missense_variant 0.16 ethambutol
embB 4249416 p.Val968Gly missense_variant 0.12 ethambutol
embB 4249628 p.Ile1039Val missense_variant 0.15 ethambutol
ethA 4326887 p.Asp196Gly missense_variant 0.19 ethionamide
ethR 4327642 p.Thr32Pro missense_variant 0.21 ethionamide
ethR 4327664 p.Asp39Ala missense_variant 0.14 ethionamide
ethA 4328442 c.-969T>G upstream_gene_variant 0.13 ethionamide
ethA 4328445 c.-972A>C upstream_gene_variant 0.35 ethionamide
ethA 4328468 c.-995T>G upstream_gene_variant 0.3 ethionamide
ethA 4328471 c.-998A>G upstream_gene_variant 0.13 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance