TB-Profiler result

Run: ERR11080959
Summary

Run ID: ERR11080959

Sample name:

Date: 07-04-2023 23:56:16

Number of reads: 5303040

Percentage reads mapped: 99.62

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 0.75
lineage4 Euro-American LAM;T;S;X;H None 0.23
lineage4.3 Euro-American (LAM) mainly-LAM None 0.21
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.77
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.77
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.25
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 761139 p.His445Tyr missense_variant 0.26 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 0.3 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.43 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.26 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 0.28
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.8
mshA 575907 p.Ala187Val missense_variant 0.77
mshA 576108 p.Ala254Gly missense_variant 0.19
ccsA 620625 p.Ile245Met missense_variant 0.78
rpoB 760644 p.Pro280Ser missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 0.72
rpoC 764995 c.1626C>G synonymous_variant 0.18
rpoC 766645 p.Glu1092Asp missense_variant 0.81
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.74
mmpL5 776182 p.Asp767Asn missense_variant 0.76
mmpS5 779615 c.-710C>G upstream_gene_variant 0.74
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 0.77
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.76
rpsA 1834836 p.Met432Thr missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 0.99
katG 2154724 p.Arg463Leu missense_variant 0.8
katG 2156196 c.-85C>T upstream_gene_variant 0.21
PPE35 2167926 p.Leu896Ser missense_variant 0.77
Rv1979c 2222112 c.1052dupT frameshift_variant 0.31
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.2
folC 2746340 p.Ala420Val missense_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 0.19
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.75
rpoA 3878618 c.-111A>C upstream_gene_variant 0.33
ddn 3986931 p.Arg30Ser missense_variant 0.33
clpC1 4038287 c.2418C>T synonymous_variant 0.23
clpC1 4038968 c.1737G>A synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 0.99
embA 4243460 c.228C>T synonymous_variant 0.71
embB 4246584 p.Arg24Pro missense_variant 0.4
aftB 4267647 p.Asp397Gly missense_variant 0.65
whiB6 4338365 p.Cys53Arg missense_variant 0.46
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.81
gid 4407927 p.Glu92Asp missense_variant 0.76
gid 4408156 p.Leu16Arg missense_variant 0.27