TB-Profiler result

Run: ERR4813613
Summary

Run ID: ERR4813613

Sample name:

Date: 01-04-2023 12:52:54

Number of reads: 4489235

Percentage reads mapped: 99.65

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 0.66
lineage4 Euro-American LAM;T;S;X;H None 0.39
lineage4.3 Euro-American (LAM) mainly-LAM None 0.39
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.65
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.64
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.37
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 0.38 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.38 isoniazid
pncA 2289213 p.Gln10Arg missense_variant 0.34 pyrazinamide
embB 4247469 p.Tyr319Ser missense_variant 0.41 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 8040 p.Gly247Ser missense_variant 0.43
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.63
mshA 575907 p.Ala187Val missense_variant 0.57
ccsA 620625 p.Ile245Met missense_variant 0.54
rpoC 763031 c.-339T>C upstream_gene_variant 0.65
rpoC 764995 c.1626C>G synonymous_variant 0.31
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.62
mmpL5 776182 p.Asp767Asn missense_variant 0.6
mmpS5 779615 c.-710C>G upstream_gene_variant 0.64
mmpS5 779630 c.-725T>C upstream_gene_variant 0.62
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.58
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.64
rpsA 1834985 c.1445dupG frameshift_variant&stop_lost&splice_region_variant 0.35
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.67
PPE35 2167926 p.Leu896Ser missense_variant 0.67
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.32
Rv2752c 3067039 c.-848T>C upstream_gene_variant 0.59
thyA 3073868 p.Thr202Ala missense_variant 0.37
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087755 c.936G>T synonymous_variant 0.69
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.71
clpC1 4038287 c.2418C>T synonymous_variant 0.44
embC 4242182 p.Ala774Ser missense_variant 0.41
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.75
embB 4249082 p.Thr857Ala missense_variant 0.67
aftB 4267647 p.Asp397Gly missense_variant 0.64
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.69
gid 4407927 p.Glu92Asp missense_variant 0.53
gid 4408156 p.Leu16Arg missense_variant 0.32