TB-Profiler result

Run: SRR25827458
Summary

Run ID: SRR25827458

Sample name:

Date: 15-03-2024 13:51:47

Number of reads: 8881351

Percentage reads mapped: 98.28

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 (0.99)
Ethambutol R embB p.Met306Val (0.70), embB p.Gly406Ala (0.35)
Pyrazinamide R pncA c.390_391dupGG (0.32), pncA c.390_391dupGG (0.32), pncA p.Ile5Thr (0.22)
Streptomycin R rpsL p.Lys43Arg (0.72)
Fluoroquinolones R gyrA p.Asp94Tyr (0.60)
Moxifloxacin R gyrA p.Asp94Tyr (0.60)
Ofloxacin R gyrA p.Asp94Tyr (0.60)
Levofloxacin R gyrA p.Asp94Tyr (0.60)
Ciprofloxacin R gyrA p.Asp94Tyr (0.60)
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 0.29
lineage2 East-Asian Beijing RD105 0.7
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.69
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.66
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 7581 p.Asp94Tyr missense_variant 0.6 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.72 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 0.32 pyrazinamide, pyrazinamide
pncA 2289228 p.Ile5Thr missense_variant 0.22 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.7 ethambutol
embB 4247730 p.Gly406Ala missense_variant 0.35 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 0.66
ccsA 620553 c.663T>C synonymous_variant 0.73
ccsA 620625 p.Ile245Met missense_variant 0.73
rpoB 759746 c.-61C>T upstream_gene_variant 0.27
rpoC 762434 c.-936T>G upstream_gene_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Ala missense_variant 0.65
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.7
mmpS5 779615 c.-710C>G upstream_gene_variant 0.77
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
rpsA 1834177 c.636A>C synonymous_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
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
pncA 2289047 c.195C>T synonymous_variant 0.35
pncA 2289365 c.-125delC upstream_gene_variant 0.33
ahpC 2726105 c.-88G>A upstream_gene_variant 0.34
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448693 p.Tyr64Asp missense_variant 0.35
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.67
fbiA 3640346 c.-196delA upstream_gene_variant 0.28
embC 4242075 p.Arg738Gln missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.75
embA 4245014 c.1782C>G synonymous_variant 0.28
embB 4249757 p.Thr1082Ala missense_variant 0.73
aftB 4267647 p.Asp397Gly missense_variant 0.62
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.68
gid 4408064 p.Arg47Gly missense_variant 0.33