TB-Profiler result

Run: ERR10748349
Summary

Run ID: ERR10748349

Sample name:

Date: 31-03-2023 10:51:39

Number of reads: 3152266

Percentage reads mapped: 99.79

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 0.17
lineage4 Euro-American LAM;T;S;X;H None 0.82
lineage4.3 Euro-American (LAM) mainly-LAM None 0.83
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.17
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.16
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.82
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 0.16 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.19 isoniazid
pncA 2288764 p.Thr160Ala missense_variant 0.17 pyrazinamide
pncA 2288943 p.Thr100Ile missense_variant 0.18 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.19 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 0.8
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491328 c.546C>G synonymous_variant 0.15
fgd1 491330 p.Lys183Met missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 0.21
mshA 575907 p.Ala187Val missense_variant 0.15
mshA 576108 p.Ala254Gly missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 0.17
rpoB 760143 p.Val113Ile missense_variant 0.79
rpoC 763031 c.-339T>C upstream_gene_variant 0.24
rpoC 764822 p.Asp485Tyr missense_variant 0.16
rpoC 764995 c.1626C>G synonymous_variant 0.83
mmpL5 775592 c.2889G>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.13
mmpL5 776182 p.Asp767Asn missense_variant 0.15
mmpL5 776689 p.Trp598Arg missense_variant 0.89
mmpS5 779615 c.-710C>G upstream_gene_variant 0.26
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.15
rpsA 1834836 p.Met432Thr missense_variant 0.8
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.24
katG 2156196 c.-85C>T upstream_gene_variant 0.87
PPE35 2167926 p.Leu896Ser missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.86
folC 2746340 p.Ala420Val missense_variant 0.87
pepQ 2860159 p.Ala87Gly missense_variant 0.24
thyA 3073868 p.Thr202Ala missense_variant 0.81
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.68
Rv3083 3449315 p.Trp271* stop_gained 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.23
Rv3236c 3612813 p.Thr102Ala missense_variant 0.11
rpoA 3878641 c.-134C>G upstream_gene_variant 0.27
clpC1 4038287 c.2418C>T synonymous_variant 0.91
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.16
embB 4246584 p.Arg24Pro missense_variant 0.2
embB 4248324 p.Ala604Gly missense_variant 0.3
aftB 4267647 p.Asp397Gly missense_variant 0.2
whiB6 4338365 p.Cys53Arg missense_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.11
gid 4407927 p.Glu92Asp missense_variant 0.16
gid 4408156 p.Leu16Arg missense_variant 0.88