TB-Profiler result

Run: SRR25827323
Summary

Run ID: SRR25827323

Sample name:

Date: 15-03-2024 08:10:35

Number of reads: 11538204

Percentage reads mapped: 98.94

Strain: lineage3;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 (0.93)
Ethambutol R embB p.Met306Val (0.90)
Pyrazinamide R pncA p.Ser59Pro (0.82)
Streptomycin R rpsL p.Lys43Arg (0.96)
Fluoroquinolones R gyrA p.Asp94Gly (0.24)
Moxifloxacin R gyrA p.Asp94Gly (0.24)
Ofloxacin R gyrA p.Asp94Gly (0.24)
Levofloxacin R gyrA p.Asp94Gly (0.24)
Ciprofloxacin R gyrA p.Asp94Gly (0.24)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid R thyX c.-16C>T (0.76)
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 0.87
lineage2 East-Asian Beijing RD105 0.05
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.08
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.11
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 0.24 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.96 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.93 isoniazid
pncA 2289067 p.Ser59Pro missense_variant 0.82 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.76 para-aminosalicylic_acid
embB 4247429 p.Met306Val missense_variant 0.9 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
ccsA 620625 p.Ile245Met missense_variant 0.17
rpoB 759746 c.-61C>T upstream_gene_variant 0.83
rpoC 762434 c.-936T>G upstream_gene_variant 0.81
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766740 p.Val1124Glu missense_variant 0.82
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 0.95
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.93
ahpC 2726105 c.-88G>A upstream_gene_variant 0.82
thyA 3074407 p.Thr22Asn missense_variant 0.83
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
Rv3236c 3612813 p.Thr102Ala missense_variant 0.12
fbiB 3642877 p.Lys448Arg missense_variant 0.8
embC 4241022 p.Ala387Val missense_variant 0.15
embC 4242075 p.Arg738Gln missense_variant 0.79
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.14
embB 4246555 c.42G>C synonymous_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 0.17
aftB 4268753 c.84T>G synonymous_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0