TB-Profiler result

Run: ERR2516985
Summary

Run ID: ERR2516985

Sample name:

Date: 31-03-2023 21:51:42

Number of reads: 4687411

Percentage reads mapped: 99.7

Strain: lineage4.6.2.2;lineage2.2.1.1

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.16
lineage4 Euro-American LAM;T;S;X;H None 0.84
lineage4.6 Euro-American T;LAM None 0.85
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.13
lineage4.6.2 Euro-American T;LAM RD726 0.88
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.14
lineage4.6.2.2 Euro-American (Cameroon) LAM10-CAM RD726 0.85
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.14
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 0.12 pyrazinamide, pyrazinamide
pncA 2289073 p.His57Asp missense_variant 0.9 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.15 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.84 ethambutol
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.16
mmpL5 776182 p.Asp767Asn missense_variant 0.17
mmpR5 778298 c.-692C>T upstream_gene_variant 0.88
mmpS5 779615 c.-710C>G upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673393 c.-809G>C upstream_gene_variant 0.93
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.13
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714846 p.Val163Ile missense_variant 0.15
folC 2746320 p.Pro427Ala missense_variant 0.77
Rv3083 3448567 p.His22Asp missense_variant 0.85
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.2
ddn 3987011 c.168C>T synonymous_variant 0.89
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.26
embB 4247880 p.Val456Ala missense_variant 0.15
embB 4248115 c.1602C>T synonymous_variant 0.12
aftB 4267272 p.Lys522Arg missense_variant 0.86
aftB 4267647 p.Asp397Gly missense_variant 0.16
ubiA 4269121 p.Phe238Ser missense_variant 0.88
ethA 4326632 p.His281Arg missense_variant 0.89
ethR 4326739 c.-810G>C upstream_gene_variant 0.9
ethA 4328004 c.-531C>T upstream_gene_variant 0.91
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.11