TB-Profiler result

Run: 11a4d724-803f-46a3-b0aa-87fddf811809
Summary

Run ID: 11a4d724-803f-46a3-b0aa-87fddf811809

Sample name:

Date: 04-03-2024 09:18:49

Number of reads: 849261

Percentage reads mapped: 98.3

Median coverage: 23

Strain: lineage4.1.1.1

Spoligotype:

Drug-resistance: Sensitive

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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
lineage4.1 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 1.0
lineage4.1.1.1 Euro-American (X-type) RD183 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
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin
amikacin
kanamycin
capreomycin
clofazimine
ethionamide
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
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 5155 c.-85G>C upstream_gene_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 6922 c.-380G>T upstream_gene_variant 0.12 fluoroquinolones
moxifloxacin
levofloxacin
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 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9601 p.Ile767Thr missense_variant 0.11 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9672 p.Val791Phe missense_variant 0.11 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9676 p.Arg792Leu missense_variant 0.11 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
fgd1 491283 p.Asp167Glu missense_variant 0.15 delamanid
fgd1 491352 p.Asp190Glu missense_variant 0.13 delamanid
fgd1 491737 p.Arg319Gly missense_variant 0.12 delamanid
mshA 575186 c.-162C>T upstream_gene_variant 0.11 ethionamide
isoniazid
mshA 575645 p.Val100Leu missense_variant 0.12 ethionamide
isoniazid Uncertain significance
mshA 575747 p.Ala134Ser missense_variant 0.14 ethionamide
isoniazid
mshA 576263 p.Leu306Met missense_variant 1.0 ethionamide
isoniazid
mshA 576789 c.1442G>T stop_lost&splice_region_variant 0.1 ethionamide
isoniazid
ccsA 619838 c.-53G>T upstream_gene_variant 0.2 capreomycin
amikacin
ccsA 620092 p.Arg68Trp missense_variant 0.1 capreomycin
amikacin
rpoB 759894 p.Pro30Ser missense_variant 0.17 rifampicin Uncertain significance
rpoB 759922 p.Arg39Leu missense_variant 0.14 rifampicin
rpoB 760972 p.Arg389Leu missense_variant 0.11 rifampicin
rpoB 760979 p.Glu391Asp missense_variant 0.1 rifampicin
rpoB 760980 c.1174C>A synonymous_variant 0.1 rifampicin
rpoB 761511 p.Glu569* stop_gained 0.11 rifampicin
rpoC 763536 p.Arg56Pro missense_variant 0.1 rifampicin
rpoC 764526 p.Arg386Leu missense_variant 0.13 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Uncertain significance
rpoC 765751 c.2382C>A synonymous_variant 0.12 rifampicin
rpoC 765868 c.2499G>T synonymous_variant 0.13 rifampicin
rpoC 767128 c.3759C>A synonymous_variant 0.17 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 778624 c.-144C>A upstream_gene_variant 0.11 clofazimine
bedaquiline
mmpS5 778712 p.Ser65Ile missense_variant 0.12 clofazimine
bedaquiline
mmpR5 779221 p.Gly78Trp missense_variant 0.11 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rplC 800639 c.-170C>G upstream_gene_variant 1.0 linezolid
fbiC 1303524 p.Trp198Cys missense_variant 0.1 delamanid
fbiC 1303835 p.Ala302Val missense_variant 0.11 delamanid
fbiC 1303840 p.Ala304Ser missense_variant 0.11 delamanid
Rv1258c 1407132 p.Gly70Glu missense_variant 0.11 streptomycin
pyrazinamide
isoniazid
embR 1416930 p.Ala140Ser missense_variant 0.11 ethambutol
atpE 1460875 c.-170C>A upstream_gene_variant 0.12 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1475031 n.1374G>T non_coding_transcript_exon_variant 0.1 linezolid
inhA 1673528 c.-674C>A upstream_gene_variant 0.1 ethionamide
isoniazid Uncertain significance
inhA 1674453 c.252G>T synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674533 p.Ala111Glu missense_variant 0.14 ethionamide
isoniazid
inhA 1674936 c.735G>T synonymous_variant 0.15 ethionamide
isoniazid
rpsA 1834604 p.Arg355Cys missense_variant 0.12 pyrazinamide
rpsA 1834664 p.Pro375Ser missense_variant 0.1 pyrazinamide
rpsA 1834735 c.1194C>A synonymous_variant 0.1 pyrazinamide
rpsA 1834921 c.1380G>T synonymous_variant 0.12 pyrazinamide
rpsA 1834943 p.Ala468Thr missense_variant 0.13 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
tlyA 1917976 c.37C>A synonymous_variant 0.17 capreomycin
tlyA 1918261 p.Val108Leu missense_variant 0.11 capreomycin
ndh 2101684 p.Gln453His missense_variant 0.1 ethionamide
isoniazid
ndh 2102251 c.792C>T synonymous_variant 0.11 ethionamide
isoniazid
ndh 2103199 c.-157G>T upstream_gene_variant 0.11 ethionamide
isoniazid
katG 2155950 c.162C>A synonymous_variant 0.11 isoniazid
katG 2156501 c.-390C>A upstream_gene_variant 0.1 isoniazid
PPE35 2169902 p.Leu237Phe missense_variant 0.19 pyrazinamide
PPE35 2169910 p.Asn235Tyr missense_variant 0.13 pyrazinamide
PPE35 2170048 p.Leu189Val missense_variant 0.18 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.11 pyrazinamide
PPE35 2170513 c.100C>T synonymous_variant 0.17 pyrazinamide
PPE35 2170518 p.Asp32Thr missense_variant 0.17 pyrazinamide
PPE35 2170525 p.Ala30Ser missense_variant 0.17 pyrazinamide
Rv1979c 2222316 c.849C>A synonymous_variant 0.11 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2290078 c.-837C>A upstream_gene_variant 0.13 pyrazinamide
kasA 2518115 p.Val1Leu missense_variant 0.11 isoniazid
kasA 2518787 c.673C>A synonymous_variant 0.12 isoniazid
kasA 2518809 p.Lys232Arg missense_variant 0.25 isoniazid
kasA 2518839 p.Ala242Gly missense_variant 0.1 isoniazid
kasA 2518879 c.765A>G synonymous_variant 0.11 isoniazid
kasA 2518882 c.768C>A synonymous_variant 0.11 isoniazid
eis 2715175 p.Gly53Asp missense_variant 0.11 kanamycin
amikacin
eis 2715558 c.-226A>C upstream_gene_variant 0.14 kanamycin
amikacin
folC 2746934 p.Arg222Leu missense_variant 0.1 para-aminosalicylic_acid
folC 2747481 p.Glu40* stop_gained 0.12 para-aminosalicylic_acid
folC 2747630 c.-32G>T upstream_gene_variant 0.1 para-aminosalicylic_acid
pepQ 2859626 p.Leu265Met missense_variant 0.2 clofazimine
bedaquiline
pepQ 2860221 c.198G>A synonymous_variant 0.12 clofazimine
bedaquiline
ribD 2987403 c.565C>A synonymous_variant 0.15 para-aminosalicylic_acid
Rv2752c 3065545 p.Ser216Ile missense_variant 0.11 rifampicin
isoniazid
Rv2752c 3065550 c.642G>T synonymous_variant 0.11 rifampicin
isoniazid
thyX 3067961 c.-16C>A upstream_gene_variant 0.1 para-aminosalicylic_acid
thyA 3073705 p.Ala256Glu missense_variant 0.12 para-aminosalicylic_acid
thyA 3073855 p.Cys206Phe missense_variant 0.11 para-aminosalicylic_acid
thyA 3074435 p.Glu13Lys missense_variant 0.2 para-aminosalicylic_acid
thyA 3074525 c.-54C>A upstream_gene_variant 0.15 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087842 c.1023A>G synonymous_variant 0.13 cycloserine
fbiD 3339194 p.Leu26Gln missense_variant 0.11 delamanid
fbiD 3339212 p.Ala32Glu missense_variant 0.11 delamanid
fbiD 3339568 p.Leu151Met missense_variant 0.11 delamanid
Rv3083 3448955 p.Pro151Gln missense_variant 0.12 ethionamide
fprA 3473975 c.-32G>T upstream_gene_variant 0.1 capreomycin
amikacin
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
fprA 3474143 p.Trp46Tyr missense_variant 0.12 capreomycin
amikacin
fprA 3474315 c.309C>A synonymous_variant 0.12 capreomycin
amikacin
fprA 3475035 p.Asn343Lys missense_variant 0.11 capreomycin
amikacin
fprA 3475045 c.1039C>A synonymous_variant 0.13 capreomycin
amikacin
fprA 3475055 p.Gly350Val missense_variant 0.13 capreomycin
amikacin
Rv3236c 3612399 p.Ala240Ser missense_variant 0.12 pyrazinamide
Rv3236c 3612600 p.Ala173Ser missense_variant 0.15 pyrazinamide
fbiB 3641130 c.-405A>T upstream_gene_variant 1.0 delamanid
fbiA 3641447 p.Thr302Met missense_variant 1.0 delamanid Uncertain significance
rpoA 3877553 p.Glu319Lys missense_variant 1.0 rifampicin Uncertain significance
rpoA 3878521 c.-14G>T upstream_gene_variant 0.12 rifampicin
ddn 3986690 c.-154C>A upstream_gene_variant 0.11 delamanid
clpC1 4038386 p.Leu773Phe missense_variant 0.11 pyrazinamide
clpC1 4039351 p.Asp452Tyr missense_variant 0.14 pyrazinamide
clpC1 4039508 c.1197G>C synonymous_variant 0.11 pyrazinamide
clpC1 4040144 c.561G>C synonymous_variant 0.22 pyrazinamide
panD 4044148 p.Thr45Asn missense_variant 0.1 pyrazinamide
embC 4240448 p.Gln196Lys missense_variant 0.1 ethambutol
embC 4240897 c.1035C>G synonymous_variant 1.0 ethambutol
embC 4242300 p.Gly813Val missense_variant 0.11 ethambutol
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Uncertain significance
embA 4242838 c.-395C>T upstream_gene_variant 1.0 ethambutol
embA 4243504 p.Ser91Tyr missense_variant 0.11 ethambutol
embA 4243526 c.294G>C synonymous_variant 0.11 ethambutol
embA 4245652 p.Thr807Asn missense_variant 0.12 ethambutol
embA 4245990 p.Pro920Thr missense_variant 0.11 ethambutol
embA 4246169 p.Met979Ile missense_variant 0.1 ethambutol
embB 4249408 c.2895G>A synonymous_variant 1.0 ethambutol
embB 4249420 c.2907G>T synonymous_variant 0.12 ethambutol
embB 4249433 p.Leu974Met missense_variant 0.13 ethambutol Uncertain significance
embB 4249465 c.2952G>T synonymous_variant 0.1 ethambutol
embB 4249696 p.Trp1061Cys missense_variant 0.12 ethambutol
aftB 4267917 c.919delA frameshift_variant 0.18 capreomycin
amikacin
aftB 4268645 c.192G>T synonymous_variant 0.12 capreomycin
amikacin
ethR 4327962 p.Trp138Cys missense_variant 0.11 ethionamide
ethA 4328461 c.-988C>T upstream_gene_variant 0.12 ethionamide
whiB6 4338292 p.Ala77Glu missense_variant 0.11 streptomycin
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407629 p.Gly192Cys missense_variant 0.1 streptomycin
gid 4408358 c.-156C>A upstream_gene_variant 0.1 streptomycin