TB-Profiler result

Run: ERR4813188

Summary

Run ID: ERR4813188

Sample name:

Date: 01-04-2023 12:35:36

Number of reads: 3325072

Percentage reads mapped: 99.67

Strain: lineage4.3.2;lineage2.2.1

Drug-resistance: Pre-XDR-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 0.9
lineage4 Euro-American LAM;T;S;X;H None 0.08
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.92
lineage4.3.2 Euro-American (LAM) LAM3 None 0.08
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.9
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
gyrA 7570 p.Ala90Val missense_variant 0.82 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.92 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.94 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.94 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.9 isoniazid
pncA 2288818 p.Thr142Ala missense_variant 0.93 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.91 ethambutol
ethA 4326305 p.Ser390Phe missense_variant 0.91 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 491742 c.960T>C synonymous_variant 0.93
mshA 575907 p.Ala187Val missense_variant 0.9
ccsA 620625 p.Ile245Met missense_variant 0.94
rpoC 763031 c.-339T>C upstream_gene_variant 0.89
rpoC 764817 p.Val483Ala missense_variant 0.92
rpoC 764995 c.1626C>G synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.94
mmpL5 776182 p.Asp767Asn missense_variant 0.93
mmpS5 779615 c.-710C>G upstream_gene_variant 0.92
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303897 c.967C>T synonymous_variant 0.9
Rv1258c 1406760 c.580_581insC frameshift_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 0.94
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.87
PPE35 2167926 p.Leu896Ser missense_variant 0.86
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 0.11
thyA 3074657 c.-186C>G upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087208 p.Leu130Pro missense_variant 0.91
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.88
clpC1 4038287 c.2418C>T synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.91
aftB 4267647 p.Asp397Gly missense_variant 0.91
whiB6 4338473 c.49A>C synonymous_variant 0.92
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.93
gid 4407927 p.Glu92Asp missense_variant 0.94
gid 4408156 p.Leu16Arg missense_variant 0.11
gid 4408413 c.-211C>T upstream_gene_variant 0.88