TB-Profiler result

Run: ERR5864679
Summary

Run ID: ERR5864679

Sample name:

Date: 01-04-2023 23:31:06

Number of reads: 1170878

Percentage reads mapped: 99.2

Strain: 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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
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 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155959 c.152delA frameshift_variant 0.12 isoniazid
pncA 2288941 c.300delC frameshift_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Val missense_variant 1.0 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576352 p.Asp335Glu missense_variant 0.12
ccsA 619983 c.93G>T synonymous_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764363 p.Gly332Cys missense_variant 1.0
rpoC 764622 p.Leu418His missense_variant 0.11
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777228 p.Arg418His missense_variant 0.1
mmpL5 778223 p.Asp86Glu missense_variant 0.1
mmpR5 779174 p.Ala62Val missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407480 c.-140A>G upstream_gene_variant 0.12
Rv1258c 1407511 c.-171T>C upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156234 c.-123G>T upstream_gene_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518155 p.Val14Ala missense_variant 0.1
folC 2746852 c.747G>T synonymous_variant 0.12
folC 2746909 c.688_689delAC frameshift_variant 0.13
folC 2746914 p.Asp229Asn missense_variant 0.13
folC 2746917 p.Pro228Ala missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087305 c.486G>T synonymous_variant 0.12
ald 3087786 p.Glu323Lys missense_variant 0.1
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612229 c.888C>T synonymous_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642229 p.Leu232Gln missense_variant 0.11
fbiB 3642232 p.Leu233Gln missense_variant 0.11
fbiB 3642234 p.Arg234Leu missense_variant 0.11
clpC1 4038269 c.2436C>G synonymous_variant 0.11
embC 4241999 c.2139delG frameshift_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247066 p.Ile185Val missense_variant 0.13
aftB 4267278 p.Arg520Gln missense_variant 0.12
aftB 4267643 c.1194C>T synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268895 c.-60delG upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0