TB-Profiler result

Run: ERR4798955

Summary

Run ID: ERR4798955

Sample name:

Date: 20-10-2023 03:26:54

Number of reads: 3944353

Percentage reads mapped: 99.6

Strain: lineage4.1.2.1;lineage3;lineage2.2.1.1

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 (0.29)
Ethambutol R embB p.Met306Val (0.18)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.20)
Fluoroquinolones R gyrA p.Asp94Gly (0.12)
Moxifloxacin R gyrA p.Asp94Gly (0.12)
Ofloxacin R gyrA p.Asp94Gly (0.12)
Levofloxacin R gyrA p.Asp94Gly (0.12)
Ciprofloxacin R gyrA p.Asp94Gly (0.12)
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
lineage3 East-African-Indian CAS RD750 0.14
lineage2 East-Asian Beijing RD105 0.2
lineage4 Euro-American LAM;T;S;X;H None 0.67
lineage4.1 Euro-American T;X;H None 0.62
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.2
lineage4.1.2 Euro-American T;H None 0.61
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.17
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.65
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.12
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 7582 p.Asp94Gly missense_variant 0.12 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpsL 781687 p.Lys43Arg missense_variant 0.2 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.29 isoniazid
embB 4247429 p.Met306Val missense_variant 0.18 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 491591 p.Lys270Met missense_variant 0.67
fgd1 491742 c.960T>C synonymous_variant 0.39
mshA 575679 p.Asn111Ser missense_variant 0.52
mshA 575907 p.Ala187Val missense_variant 0.17
ccsA 620625 p.Ile245Met missense_variant 0.23
rpoB 759746 c.-61C>T upstream_gene_variant 0.14
rpoB 760061 c.255C>T synonymous_variant 0.63
rpoB 760115 c.309C>T synonymous_variant 0.64
rpoC 762434 c.-936T>G upstream_gene_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 0.41
rpoC 764363 p.Gly332Ser missense_variant 0.19
rpoC 765150 p.Gly594Glu missense_variant 0.62
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.37
mmpL5 776182 p.Asp767Asn missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302920 c.-11G>A upstream_gene_variant 0.74
Rv1258c 1406760 c.580_581insC frameshift_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673204 c.-236C>T upstream_gene_variant 0.16
rpsA 1834177 c.636A>C synonymous_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.36
PPE35 2167926 p.Leu896Ser missense_variant 0.36
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288755 p.Val163Met missense_variant 0.67
pncA 2289047 c.195C>T synonymous_variant 0.15
pncA 2289365 c.-125delC upstream_gene_variant 0.15
kasA 2518076 c.-39C>T upstream_gene_variant 0.58
ahpC 2726105 c.-88G>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
Rv3236c 3612813 p.Thr102Ala missense_variant 0.16
fbiB 3641490 c.-45G>A upstream_gene_variant 0.62
rpoA 3878586 c.-79A>G upstream_gene_variant 0.32
embC 4242075 p.Arg738Gln missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.6
embA 4243460 c.228C>T synonymous_variant 0.19
aftB 4267647 p.Asp397Gly missense_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.32
gid 4407927 p.Glu92Asp missense_variant 0.16