TB-Profiler result

Run: ERR2512780
Summary

Run ID: ERR2512780

Sample name:

Date: 20-10-2023 12:53:46

Number of reads: 3003542

Percentage reads mapped: 99.44

Strain: lineage6.1.3;lineage2.2.1

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R katG p.Ser315Thr (0.67)
Ethambutol R embC p.Ala307Thr (0.38)
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
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 0.71
lineage6 West-Africa 2 AFRI_1 RD702 0.33
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.7
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.68
lineage6.1.3 West-Africa 2 AFRI_1 RD702 0.34
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
katG 2155168 p.Ser315Thr missense_variant 0.67 isoniazid
embC 4240781 p.Ala307Thr missense_variant 0.38 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
gyrB 6446 p.Ala403Ser missense_variant 0.31
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8493 p.Leu398Phe missense_variant 0.23
gyrA 8806 p.Asp502Gly missense_variant 0.3
gyrA 9143 c.1842T>C synonymous_variant 0.36
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491668 p.Lys296Glu missense_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 0.64
ccsA 620625 p.Ile245Met missense_variant 0.65
rpoB 760855 p.Thr350Ile missense_variant 0.26
rpoB 760969 p.Ser388Leu missense_variant 0.31
rpoB 761723 p.Glu639Asp missense_variant 0.41
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766231 c.2862T>C synonymous_variant 0.28
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.54
mmpS5 779615 c.-710C>G upstream_gene_variant 0.7
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302899 c.-32A>G upstream_gene_variant 0.4
Rv1258c 1406253 p.Gly363Val missense_variant 0.66
Rv1258c 1406685 p.Val219Ala missense_variant 0.3
Rv1258c 1406760 c.580_581insC frameshift_variant 0.7
embR 1416633 p.Leu239Val missense_variant 0.27
atpE 1461251 c.207G>T synonymous_variant 0.34
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472912 n.1067C>T non_coding_transcript_exon_variant 0.65
rrl 1473633 n.-25C>T upstream_gene_variant 0.32
inhA 1674210 c.9A>C synonymous_variant 0.72
inhA 1674434 p.Val78Ala missense_variant 0.39
rpsA 1834177 c.636A>C synonymous_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155503 c.609C>T synonymous_variant 0.28
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 0.3
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.35
folC 2747727 c.-129C>G upstream_gene_variant 0.69
ald 3086728 c.-92C>T upstream_gene_variant 0.34
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087084 c.266delA frameshift_variant 0.36
ald 3087412 p.Asp198Val missense_variant 0.27
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.3
Rv3236c 3612143 p.Arg325His missense_variant 0.26
Rv3236c 3612813 p.Thr102Ala missense_variant 0.76
rpoA 3877740 c.768G>C synonymous_variant 0.31
embC 4241843 p.Leu661Ile missense_variant 0.36
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.68
embA 4244220 c.988C>T synonymous_variant 0.32
embA 4244379 p.Pro383Ser missense_variant 0.39
embB 4246864 c.351C>T synonymous_variant 0.3
embB 4247646 p.Glu378Ala missense_variant 0.28
aftB 4267647 p.Asp397Gly missense_variant 0.64
aftB 4269351 c.-515C>T upstream_gene_variant 0.31
ubiA 4269387 p.Glu149Asp missense_variant 0.37
aftB 4269522 c.-686C>T upstream_gene_variant 0.33
aftB 4269606 c.-770T>C upstream_gene_variant 0.27
ethA 4326465 p.Ile337Val missense_variant 0.3
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338602 c.-81A>C upstream_gene_variant 0.28
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.66
gid 4408034 p.Glu57Lys missense_variant 0.26