TB-Profiler result

Run: ERR10112894
Summary

Run ID: ERR10112894

Sample name:

Date: 19-05-2023 07:21:10

Number of reads: 1232465

Percentage reads mapped: 99.62

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
Rifampicin R rpoB p.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (1.00)
Ethambutol
Pyrazinamide R pncA p.Tyr103* (0.12)
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), ethR p.Ala95Thr (1.00)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
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 0.99
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2288933 p.Tyr103* stop_gained 0.12 pyrazinamide
ethR 4327831 p.Ala95Thr missense_variant 1.0 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
gyrA 9319 p.Leu673Pro missense_variant 0.1
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.24
mshA 576461 p.Ala372Thr missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760461 p.Arg219Cys missense_variant 0.35
rpoB 760719 p.Val305Ile missense_variant 0.25
rpoB 761278 p.Ile491Thr missense_variant 0.1
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_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
mmpR5 778247 c.-743G>A upstream_gene_variant 0.12
mmpS5 778979 c.-74G>T upstream_gene_variant 1.0
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473626 n.-32C>G upstream_gene_variant 0.18
rrl 1475573 n.1921delC non_coding_transcript_exon_variant 0.2
rrl 1476011 n.2354A>T non_coding_transcript_exon_variant 0.11
rrl 1476203 n.2546G>T non_coding_transcript_exon_variant 0.17
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 2155885 p.Leu76Pro missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170065 p.Ala183Gly missense_variant 0.23
Rv1979c 2221861 p.Arg435Leu missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860159 p.Ala87Gly missense_variant 0.29
pepQ 2860543 c.-125A>C upstream_gene_variant 0.11
thyX 3068114 c.-169G>A upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.86
fbiD 3339746 p.Ala210Gly missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568428 c.252A>G synonymous_variant 0.25
whiB7 3568718 c.-39A>T upstream_gene_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embC 4240409 p.Pro183Ala missense_variant 0.23
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4248319 c.1806A>T synonymous_variant 0.2
embB 4248324 p.Ala604Gly missense_variant 0.3
embB 4248328 c.1815G>C synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268619 p.Val73Gly missense_variant 0.3
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