TB-Profiler result

Run: ERR229930
Summary

Run ID: ERR229930

Sample name:

Date: 31-03-2023 17:52:25

Number of reads: 4418316

Percentage reads mapped: 99.56

Strain: lineage4.1.2.1;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 0.85
lineage4 Euro-American LAM;T;S;X;H None 0.14
lineage4.1 Euro-American T;X;H None 0.15
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.87
lineage4.1.2 Euro-American T;H None 0.13
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.87
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 0.83 rifampicin
rpoB 762089 p.Glu761Asp missense_variant 0.81 rifampicin
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.75 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.8 isoniazid
eis 2715369 c.-37G>T upstream_gene_variant 0.72 kanamycin
embB 4247574 p.Asp354Ala missense_variant 0.78 ethambutol
ethA 4327480 c.-7T>C upstream_gene_variant 0.87 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 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 0.83
mshA 575907 p.Ala187Val missense_variant 0.83
ccsA 620625 p.Ile245Met missense_variant 0.83
rpoC 763031 c.-339T>C upstream_gene_variant 0.8
rpoC 765150 p.Gly594Glu missense_variant 0.13
rpoC 766645 p.Glu1092Asp missense_variant 0.85
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.84
mmpL5 776182 p.Asp767Asn missense_variant 0.86
mmpS5 779615 c.-710C>G upstream_gene_variant 0.81
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.9
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.89
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.86
PPE35 2167926 p.Leu896Ser missense_variant 0.87
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289226 p.Ile6Leu missense_variant 0.72
kasA 2518076 c.-39C>T upstream_gene_variant 0.16
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.87
embC 4242425 p.Arg855Gly missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.11
embA 4243460 c.228C>T synonymous_variant 0.88
aftB 4267647 p.Asp397Gly missense_variant 0.96
whiB6 4338371 p.Thr51Pro missense_variant 0.11
whiB6 4338513 c.9C>T synonymous_variant 0.13
whiB6 4338563 c.-42G>T upstream_gene_variant 0.79
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.9
gid 4407927 p.Glu92Asp missense_variant 0.75