TB-Profiler result

Run: ERR10748557
Summary

Run ID: ERR10748557

Sample name:

Date: 31-03-2023 10:58:44

Number of reads: 2632444

Percentage reads mapped: 99.25

Strain: lineage4.3.2.1;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 0.83
lineage4 Euro-American LAM;T;S;X;H None 0.16
lineage4.3 Euro-American (LAM) mainly-LAM None 0.12
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.81
lineage4.3.2 Euro-American (LAM) LAM3 None 0.16
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.78
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.14
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 0.82 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.92 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 0.75 isoniazid, ethionamide
katG 2155169 p.Ser315Gly missense_variant 0.11 isoniazid
pncA 2289220 p.Asp8Asn missense_variant 0.81 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.87 ethambutol
ethR 4327831 p.Ala95Thr missense_variant 0.95 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
gyrB 5520 p.Pro94Leu missense_variant 0.17
gyrA 7222 c.-80C>T upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.84
mshA 575907 p.Ala187Val missense_variant 0.8
mshA 576108 p.Ala254Gly missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 0.84
rpoC 763031 c.-339T>C upstream_gene_variant 0.84
rpoC 763555 c.186C>T synonymous_variant 0.86
rpoC 764822 p.Asp485Tyr missense_variant 0.78
rpoC 764995 c.1626C>G synonymous_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.82
mmpL5 776182 p.Asp767Asn missense_variant 0.8
mmpS5 778979 c.-74G>T upstream_gene_variant 0.79
mmpS5 779615 c.-710C>G upstream_gene_variant 0.9
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.76
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 0.81
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.78
PPE35 2167926 p.Leu896Ser missense_variant 0.83
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.16
thyA 3073868 p.Thr202Ala missense_variant 0.21
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.92
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.83
rpoA 3878597 c.-90G>C upstream_gene_variant 0.3
clpC1 4038287 c.2418C>T synonymous_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.87
embB 4248324 p.Ala604Gly missense_variant 0.24
aftB 4267647 p.Asp397Gly missense_variant 0.87
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.82
gid 4407927 p.Glu92Asp missense_variant 0.8
gid 4408156 p.Leu16Arg missense_variant 0.12