TB-Profiler result

Run: ERR4812079
Summary

Run ID: ERR4812079

Sample name:

Date: 01-04-2023 11:50:52

Number of reads: 3929215

Percentage reads mapped: 99.73

Strain: lineage4.3.3;lineage2.2.1

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 0.24
lineage4 Euro-American LAM;T;S;X;H None 0.79
lineage4.3 Euro-American (LAM) mainly-LAM None 0.79
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.21
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.22
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.8
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 761110 p.Asp435Val missense_variant 0.78 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.8 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 0.79 pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 0.76 ethambutol
gid 4407952 p.Pro84Leu missense_variant 0.81 streptomycin
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 8040 p.Gly247Ser missense_variant 0.78
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.18
mshA 575907 p.Ala187Val missense_variant 0.26
ccsA 620625 p.Ile245Met missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 0.21
rpoC 764995 c.1626C>G synonymous_variant 0.78
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.22
mmpL5 776182 p.Asp767Asn missense_variant 0.21
mmpS5 779615 c.-710C>G upstream_gene_variant 0.23
mmpS5 779630 c.-725T>C upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.2
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 0.73
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.28
PPE35 2167926 p.Leu896Ser missense_variant 0.21
PPE35 2168998 p.Ile539Val missense_variant 0.74
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.84
Rv2752c 3067039 c.-848T>C upstream_gene_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 0.75
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087755 c.936G>T synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.28
clpC1 4038287 c.2418C>T synonymous_variant 0.83
embC 4242182 p.Ala774Ser missense_variant 0.76
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.32
embB 4246584 p.Arg24Pro missense_variant 0.26
aftB 4267647 p.Asp397Gly missense_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.17
gid 4407927 p.Glu92Asp missense_variant 0.21
gid 4408156 p.Leu16Arg missense_variant 0.78