TB-Profiler result

Run: ERR11465157
Summary

Run ID: ERR11465157

Sample name:

Date: 09-01-2024 19:00:41

Number of reads: 4667143

Percentage reads mapped: 99.57

Strain: lineage4.3.2.1;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
Rifampicin R rpoB p.Ser450Leu (0.77)
Isoniazid R katG p.Ser315Thr (0.57)
Ethambutol R embB p.Met306Val (0.65)
Pyrazinamide R pncA p.Ala28Asp (0.60)
Streptomycin R rpsL p.Lys43Arg (0.74)
Fluoroquinolones R gyrB p.Ala504Val (0.65)
Moxifloxacin R gyrB p.Ala504Val (0.65)
Ofloxacin R gyrB p.Ala504Val (0.65)
Levofloxacin R gyrB p.Ala504Val (0.65)
Ciprofloxacin R gyrB p.Ala504Val (0.65)
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 0.62
lineage4 Euro-American LAM;T;S;X;H None 0.39
lineage4.3 Euro-American (LAM) mainly-LAM None 0.35
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.65
lineage4.3.2 Euro-American (LAM) LAM3 None 0.33
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.64
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.35
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
gyrB 6750 p.Ala504Val missense_variant 0.65 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.77 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.74 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.57 isoniazid
pncA 2289159 p.Ala28Asp missense_variant 0.6 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.65 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 5520 p.Pro94Leu missense_variant 0.32
gyrA 7222 c.-80C>T upstream_gene_variant 0.52
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 0.67
mshA 575907 p.Ala187Val missense_variant 0.81
ccsA 620625 p.Ile245Met missense_variant 0.66
rpoC 763031 c.-339T>C upstream_gene_variant 0.56
rpoC 764995 c.1626C>G synonymous_variant 0.33
rpoC 766645 p.Glu1092Asp missense_variant 0.58
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.73
mmpL5 776182 p.Asp767Asn missense_variant 0.68
mmpS5 779615 c.-710C>G upstream_gene_variant 0.61
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.72
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.36
rpsA 1834177 c.636A>C synonymous_variant 0.61
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.7
PPE35 2167926 p.Leu896Ser missense_variant 0.59
PPE35 2169902 c.711G>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073715 p.Pro253Ala missense_variant 0.59
thyA 3073868 p.Thr202Ala missense_variant 0.41
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568795 c.-116A>G upstream_gene_variant 0.56
Rv3236c 3612813 p.Thr102Ala missense_variant 0.64
rpoA 3877949 p.Thr187Ala missense_variant 0.65
clpC1 4038287 c.2418C>T synonymous_variant 0.35
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.76
aftB 4267647 p.Asp397Gly missense_variant 0.65
ethA 4326533 p.Thr314Ile missense_variant 0.67
whiB6 4338365 p.Cys53Arg missense_variant 0.51
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.79
gid 4407927 p.Glu92Asp missense_variant 0.72
gid 4408156 p.Leu16Arg missense_variant 0.28