TB-Profiler result

Run: SRR20969464
Summary

Run ID: SRR20969464

Sample name:

Date: 2024-10-05T01:00:19.095585

Number of reads: 10383786

Percentage reads mapped: 99.64

Median coverage: 275.0

Strain: lineage2.2.1;lineage4.5

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.5 Euro-American RD122 0.19
lineage2 East-Asian RD105 0.81
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.8
lineage2.2 East-Asian (Beijing) RD105;RD207 0.79
lineage4 Euro-American None 0.19
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
rpoC p.Gly332Arg Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
pyrazinamide pncA c.386_388delATG Mutation from literature
streptomycin gid c.102delG Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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 761155 p.Ser450Leu missense_variant 0.2 rifampicin Assoc w R
rpoC 764363 p.Gly332Arg missense_variant 0.23 rifampicin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.15 isoniazid Assoc w R High-level resistance
pncA 2288853 c.386_388delATG disruptive_inframe_deletion 0.19 pyrazinamide Mutation from literature
embA 4243221 c.-12C>T upstream_gene_variant 0.16 ethambutol Uncertain significance Mutation from literature
gid 4408100 c.102delG frameshift_variant 0.18 streptomycin Assoc w R
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 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7892 c.591G>A synonymous_variant 0.2 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.82 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.79 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620029 c.139C>T synonymous_variant 0.25 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.79 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.81 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.8 ethionamide Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.79 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.83 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.76 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.84 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.8 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.81 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1473294 n.1449A>C non_coding_transcript_exon_variant 0.23 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1833701 p.Asp54Asn missense_variant 0.19 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.8 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.81 isoniazid Not assoc w R
katG 2155677 c.435C>A synonymous_variant 0.19 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.82 pyrazinamide Not assoc w R
PPE35 2170568 p.Ile15Met missense_variant 0.21 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv2680 2996411 p.Val103Leu missense_variant 0.81 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 0.77 cycloserine
fbiD 3339480 p.Gln121His missense_variant 0.19 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
Rv3083 3448508 p.Asn2Ser missense_variant 0.82 ethionamide
Rv3236c 3612813 p.Thr102Ala missense_variant 0.8 pyrazinamide Not assoc w R - Interim
lpqB 3623178 p.Ala578Val missense_variant 0.76 rifampicin
bedaquiline
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.82 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878575 c.-68C>T upstream_gene_variant 0.28 rifampicin Not assoc w R
ddn 3987001 p.Gly53Asp missense_variant 0.14 pretomanid
delamanid Uncertain significance
clpC1 4038318 p.Pro796Leu missense_variant 0.17 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.79 ethambutol Not assoc w R
embB 4247841 p.Gly443Asp missense_variant 0.17 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.84 ethambutol Not assoc w R
ethA 4327875 c.-402C>A upstream_gene_variant 0.16 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.82 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.77 streptomycin Not assoc w R