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Detailed information for vg0408266266:

Variant ID: vg0408266266 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 8266266
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:


AGCCTTCTCGGCGAGGTCAACCGAGTTTTGGCACGGTTGATAACCAGAGGAGATGTGATGCTGTGATTGCGGGGCTCAGTAGCGTGTTCGTTCAAAAGCC[G/A]
GATCGAGTTGTGTCACGACTCCGCCCAAATCGACTGTTTATCAATACCTATCGGAACATCGGGACCTATTCCCCATCACAATGACTCATTCATTTTGTTT

Reverse complement sequence

AAACAAAATGAATGAGTCATTGTGATGGGGAATAGGTCCCGATGTTCCGATAGGTATTGATAAACAGTCGATTTGGGCGGAGTCGTGACACAACTCGATC[C/T]
GGCTTTTGAACGAACACGCTACTGAGCCCCGCAATCACAGCATCACATCTCCTCTGGTTATCAACCGTGCCAAAACTCGGTTGACCTCGCCGAGAAGGCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.20% 23.70% 0.06% 0.00% NA
All Indica  2759 94.00% 5.90% 0.07% 0.00% NA
All Japonica  1512 38.20% 61.80% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 76.80% 23.20% 0.00% 0.00% NA
Indica III  913 97.00% 3.00% 0.00% 0.00% NA
Indica Intermediate  786 96.30% 3.60% 0.13% 0.00% NA
Temperate Japonica  767 4.20% 95.80% 0.00% 0.00% NA
Tropical Japonica  504 93.50% 6.50% 0.00% 0.00% NA
Japonica Intermediate  241 31.10% 68.90% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 74.40% 24.40% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0408266266 G -> A LOC_Os04g14710.1 intron_variant ; MODIFIER silent_mutation Average:31.607; most accessible tissue: Callus, score: 58.332 N N N N
vg0408266266 G -> A LOC_Os04g14710.2 intron_variant ; MODIFIER silent_mutation Average:31.607; most accessible tissue: Callus, score: 58.332 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0408266266 NA 4.84E-07 mr1715 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0408266266 NA 8.21E-07 mr1739 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0408266266 NA 7.26E-07 mr1826 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0408266266 NA 3.90E-09 mr1959 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0408266266 NA 1.30E-07 mr1993 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0408266266 NA 7.86E-12 mr1378_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0408266266 NA 8.02E-16 mr1520_2 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251