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Detailed information for vg0308476883:

Variant ID: vg0308476883 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 8476883
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.22, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


CATCAAAGGCCAGCAGGCTTACTCCAACCCCTTCAAATCCCGGAATGGAAATGGGAAGAAATCGGAATGGATTTCATAACAGGTTTGCCCAGGACATCGT[T/C]
GGGGCACGATTCAATCTGGGTGGTCGTGGATCGACTCACCAAAGTTGCTCATTTCATTCCAGTACACACTACCTATACCGGGAAAAGGTTGGCAGAGCTT

Reverse complement sequence

AAGCTCTGCCAACCTTTTCCCGGTATAGGTAGTGTGTACTGGAATGAAATGAGCAACTTTGGTGAGTCGATCCACGACCACCCAGATTGAATCGTGCCCC[A/G]
ACGATGTCCTGGGCAAACCTGTTATGAAATCCATTCCGATTTCTTCCCATTTCCATTCCGGGATTTGAAGGGGTTGGAGTAAGCCTGCTGGCCTTTGATG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 11.10% 1.20% 36.25% 51.52% NA
All Indica  2759 4.10% 2.00% 46.25% 47.73% NA
All Japonica  1512 25.50% 0.00% 18.06% 56.48% NA
Aus  269 1.90% 0.40% 20.82% 76.95% NA
Indica I  595 1.00% 2.40% 22.02% 74.62% NA
Indica II  465 7.30% 1.30% 49.25% 42.15% NA
Indica III  913 3.30% 1.50% 61.12% 34.06% NA
Indica Intermediate  786 5.30% 2.50% 45.55% 46.56% NA
Temperate Japonica  767 45.40% 0.00% 12.91% 41.72% NA
Tropical Japonica  504 4.00% 0.00% 25.60% 70.44% NA
Japonica Intermediate  241 7.10% 0.00% 18.67% 74.27% NA
VI/Aromatic  96 5.20% 0.00% 65.62% 29.17% NA
Intermediate  90 17.80% 0.00% 50.00% 32.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0308476883 T -> C LOC_Os03g15450.1 intron_variant ; MODIFIER silent_mutation Average:13.986; most accessible tissue: Minghui63 root, score: 25.504 N N N N
vg0308476883 T -> DEL N N silent_mutation Average:13.986; most accessible tissue: Minghui63 root, score: 25.504 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0308476883 NA 3.95E-06 mr1026 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
vg0308476883 NA 9.32E-06 mr1192 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
vg0308476883 NA 1.06E-06 mr1330 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
vg0308476883 NA 5.24E-09 mr1627 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
vg0308476883 NA 1.19E-10 mr1712 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
vg0308476883 1.52E-07 NA mr1779 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
vg0308476883 7.77E-08 7.77E-08 mr1779 Jap_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
vg0308476883 NA 3.55E-08 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
vg0308476883 NA 8.87E-06 mr1910 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
vg0308476883 NA 9.77E-09 mr1977 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
vg0308476883 NA 8.67E-07 mr1977 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
vg0308476883 6.74E-06 NA mr1933_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