TB-Profiler result

Run: ERR4797409

Summary

Run ID: ERR4797409

Sample name:

Date: 20-10-2023 02:20:11

Number of reads: 5716233

Percentage reads mapped: 99.6

Strain: lineage3;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.His445Asn (0.87)
Isoniazid R katG p.Ser315Thr (0.12)
Ethambutol R embB p.Met306Val (0.10)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.13)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.593delG (0.12)
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.14)
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 0.88
lineage2 East-Asian Beijing RD105 0.12
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.1
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.08
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 761139 p.His445Asn missense_variant 0.87 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.13 streptomycin
katG 2155167 p.Ser315Thr missense_variant 0.12 isoniazid
thyX 3067961 c.-16C>T upstream_gene_variant 0.14 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.1 ethambutol
ethA 4326880 c.593delG frameshift_variant 0.12 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 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 0.82
rpoC 762434 c.-936T>G upstream_gene_variant 0.82
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472653 n.808C>T non_coding_transcript_exon_variant 0.84
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.89
pncA 2289365 c.-125delC upstream_gene_variant 0.87
ahpC 2726105 c.-88G>A upstream_gene_variant 0.95
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 0.11
embC 4242075 p.Arg738Gln missense_variant 0.92
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_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 0.12