TB-Profiler result

Run: ERR133821
Summary

Run ID: ERR133821

Sample name:

Date: 31-03-2023 13:36:44

Number of reads: 19569052

Percentage reads mapped: 99.67

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 0.32
lineage4 Euro-American LAM;T;S;X;H None 0.66
lineage4.3 Euro-American (LAM) mainly-LAM None 0.66
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.32
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.33
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.66
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 0.34 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.27 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.35 isoniazid
pncA 2289207 p.Asp12Ala missense_variant 0.3 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.37 kanamycin
embB 4247730 p.Gly406Ala missense_variant 0.34 ethambutol
ethA 4326183 c.1290delC frameshift_variant 0.27 ethionamide, ethionamide
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 0.98
gyrA 8040 p.Gly247Ser missense_variant 0.67
gyrA 8562 c.1261C>T synonymous_variant 0.72
gyrA 9304 p.Gly668Asp missense_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 0.31
mshA 575907 p.Ala187Val missense_variant 0.32
ccsA 620625 p.Ile245Met missense_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 0.33
rpoC 764703 p.Lys445Arg missense_variant 0.29
rpoC 764809 c.1440C>T synonymous_variant 0.68
rpoC 764995 c.1626C>G synonymous_variant 0.66
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.33
mmpL5 776182 p.Asp767Asn missense_variant 0.33
mmpS5 779615 c.-710C>G upstream_gene_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.35
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.3
rpsA 1834836 p.Met432Thr missense_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.29
katG 2156196 c.-85C>T upstream_gene_variant 0.69
PPE35 2167926 p.Leu896Ser missense_variant 0.29
PPE35 2169122 c.1491C>G synonymous_variant 0.7
PPE35 2169125 p.Val496Ile missense_variant 0.7
PPE35 2169320 p.Leu431Phe missense_variant 0.24
PPE35 2169866 c.747G>C synonymous_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.69
folC 2746340 p.Ala420Val missense_variant 0.63
ribD 2987307 p.Ala157Pro missense_variant 0.21
thyA 3073868 p.Thr202Ala missense_variant 0.65
ald 3086731 c.-89A>G upstream_gene_variant 0.32
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
fprA 3475189 p.Cys395Gly missense_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 0.31
clpC1 4038287 c.2418C>T synonymous_variant 0.63
clpC1 4038857 c.1848C>A synonymous_variant 0.28
clpC1 4038968 c.1737G>A synonymous_variant 0.67
embC 4239842 c.-21C>A upstream_gene_variant 0.21
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4243346 c.114A>G synonymous_variant 0.35
embA 4243460 c.228C>T synonymous_variant 0.35
aftB 4267647 p.Asp397Gly missense_variant 0.33
whiB6 4338371 p.Thr51Pro missense_variant 0.32
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.34
gid 4407927 p.Glu92Asp missense_variant 0.33
gid 4408156 p.Leu16Arg missense_variant 0.65