TB-Profiler result

Run: ERR234601
Summary

Run ID: ERR234601

Sample name:

Date: 21-10-2023 06:02:24

Number of reads: 4348207

Percentage reads mapped: 99.58

Strain: 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 (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (0.49)
Pyrazinamide R pncA p.His51Pro (0.51)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrA p.Asp94Ala (0.47)
Moxifloxacin R gyrA p.Asp94Ala (0.47)
Ofloxacin R gyrA p.Asp94Ala (0.47)
Levofloxacin R gyrA p.Asp94Ala (0.47)
Ciprofloxacin R gyrA p.Asp94Ala (0.47)
Aminoglycosides
Amikacin R eis c.-14C>T (0.63)
Capreomycin
Kanamycin R eis c.-14C>T (0.63)
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid R folC p.Ile43Thr (0.56)
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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 1.0
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.Asp94Ala missense_variant 0.47 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289090 p.His51Pro missense_variant 0.51 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 0.63 kanamycin, amikacin
folC 2747471 p.Ile43Thr missense_variant 0.56 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.49 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 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764714 p.Leu449Val missense_variant 0.38
rpoC 764817 p.Val483Gly missense_variant 0.58
rpoC 766645 p.Glu1092Asp missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918100 p.Val54Gly missense_variant 0.57
tlyA 1918164 c.229_234dupTTCGCG conservative_inframe_insertion 0.4
tlyA 1918174 p.Ile79Phe missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073715 p.Pro253Ala missense_variant 0.49
ald 3086731 c.-89A>G upstream_gene_variant 0.64
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568734 c.-55G>T upstream_gene_variant 0.45
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841356 p.Ser22Leu missense_variant 0.43
clpC1 4039176 p.Met510Thr missense_variant 0.54
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 0.61
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269116 p.Arg240Cys missense_variant 0.5
ethA 4326533 p.Thr314Ile missense_variant 0.4
ethA 4327004 p.Phe157Ser missense_variant 0.55
whiB6 4338371 p.Thr51Pro missense_variant 0.58
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0