TB-Profiler result

Run: 3ca006ee-2d12-48e5-8b82-858896d0df60
Summary

Run ID: 3ca006ee-2d12-48e5-8b82-858896d0df60

Sample name:

Date: 21-12-2023 04:56:46

Number of reads: 2025906

Percentage reads mapped: 92.87

Median coverage: 62

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.98
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.98
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
gyrA 6904 c.-398C>G upstream_gene_variant 0.11 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 6910 c.-392G>A upstream_gene_variant 0.12 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 6911 p.Asn558His missense_variant 0.12 fluoroquinolones
moxifloxacin
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 6919 c.-383T>C upstream_gene_variant 0.12 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 6925 c.-377T>C upstream_gene_variant 0.11 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 6931 c.-371A>C upstream_gene_variant 0.1 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 6934 c.-368A>G upstream_gene_variant 0.13 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 0.98 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
fgd1 491742 c.960T>C synonymous_variant 1.0 delamanid
rpoB 760283 c.477G>C synonymous_variant 0.11 rifampicin
rpoB 760307 c.501T>C synonymous_variant 0.11 rifampicin
rpoB 761021 c.1215G>C synonymous_variant 0.1 rifampicin
rpoB 761027 c.1221A>G synonymous_variant 0.1 rifampicin
rpoB 761058 p.Val418Met missense_variant 0.91 rifampicin
rpoB 761097 c.1291_1292delAGinsTC synonymous_variant 0.1 rifampicin
rpoB 761150 c.1344A>C synonymous_variant 0.12 rifampicin
rpoB 761165 c.1359G>C synonymous_variant 0.1 rifampicin
rpoB 761168 c.1362C>G synonymous_variant 0.1 rifampicin
rpoB 761183 c.1377T>G synonymous_variant 0.11 rifampicin
rpoB 761189 c.1383T>G synonymous_variant 0.1 rifampicin
rpoC 762989 c.-381G>C upstream_gene_variant 0.11 rifampicin
rpoC 762995 c.-375G>T upstream_gene_variant 0.11 rifampicin
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
rpoC 764764 c.1395T>C synonymous_variant 0.1 rifampicin
rpoC 764809 c.1440C>T synonymous_variant 0.11 rifampicin
rpoC 764812 c.1443C>G synonymous_variant 0.11 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.11 rifampicin
rpoC 764824 c.1455T>C synonymous_variant 0.1 rifampicin
rpoC 765826 c.2457T>C synonymous_variant 0.11 rifampicin
rpoC 765835 c.2466C>T synonymous_variant 0.11 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.11 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.11 rifampicin
rpoC 765928 c.2559C>G synonymous_variant 0.1 rifampicin
rpoC 765967 c.2598C>T synonymous_variant 0.13 rifampicin
rpoC 765979 c.2610C>G synonymous_variant 0.11 rifampicin
rpoC 765982 c.2613C>T synonymous_variant 0.11 rifampicin
rpoC 765985 c.2616C>T synonymous_variant 0.11 rifampicin
rpoC 765994 c.2625A>T synonymous_variant 0.13 rifampicin
rpoC 766009 c.2640G>C synonymous_variant 0.13 rifampicin
rpoC 766010 c.2641_2642delTCinsAG synonymous_variant 0.13 rifampicin
rpoC 766021 c.2652G>C synonymous_variant 0.15 rifampicin
rpoC 766043 p.Gln892Glu missense_variant 0.11 rifampicin
rpoC 766054 c.2685C>G synonymous_variant 0.12 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.1 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.1 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
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
rplC 800703 c.-106T>C upstream_gene_variant 0.1 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.1 linezolid
rplC 800738 c.-71T>C upstream_gene_variant 0.11 linezolid
rplC 800747 c.-62C>G upstream_gene_variant 0.11 linezolid
rplC 800771 c.-38C>T upstream_gene_variant 0.11 linezolid
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1473893 n.236T>C non_coding_transcript_exon_variant 0.94 linezolid Uncertain significance
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.11 linezolid Uncertain significance
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.14 linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.13 linezolid
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.1 linezolid
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.1 linezolid
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.1 linezolid
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.1 linezolid
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
ndh 2101891 c.1152C>A synonymous_variant 1.0 ethionamide
isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169666 p.Asn316Ile missense_variant 1.0 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Uncertain significance
fbiB 3640776 c.-759C>T upstream_gene_variant 1.0 delamanid
fbiB 3640879 c.-656C>T upstream_gene_variant 1.0 delamanid
rpoA 3878169 c.339G>C synonymous_variant 0.1 rifampicin
clpC1 4038596 c.2109A>G synonymous_variant 0.1 pyrazinamide
clpC1 4038740 c.1965G>C synonymous_variant 0.14 pyrazinamide
clpC1 4038755 c.1950G>C synonymous_variant 0.14 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.12 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.13 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.12 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.11 pyrazinamide
clpC1 4039073 c.1632C>G synonymous_variant 0.11 pyrazinamide
clpC1 4039085 c.1620A>G synonymous_variant 0.12 pyrazinamide
clpC1 4039090 c.1615C>T synonymous_variant 0.12 pyrazinamide
clpC1 4039112 c.1593C>G synonymous_variant 0.1 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.11 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.1 pyrazinamide
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
ethA 4326474 p.Pro334Ala missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338595 c.-75delG 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 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Uncertain significance