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Detailed information for vg0506745303:

Variant ID: vg0506745303 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6745303
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, C: 0.06, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


AAAAGGAGAAAAACATACGAACAACGGCAATGGGCGAGAAATATCAAATCAATGTAATTTAAGAGGGGTATTTACAATGAATTATTTGGGGAAATATCAA[A/C]
CTCAAGATGATATTTGGGATGGTTTTTATGATTTTCCCTTATGTCATCTTCTTCTTTTGTGAGACTGATGCTCTATACATGTGCCGAGTTGTCTATACCA

Reverse complement sequence

TGGTATAGACAACTCGGCACATGTATAGAGCATCAGTCTCACAAAAGAAGAAGATGACATAAGGGAAAATCATAAAAACCATCCCAAATATCATCTTGAG[T/G]
TTGATATTTCCCCAAATAATTCATTGTAAATACCCCTCTTAAATTACATTGATTTGATATTTCTCGCCCATTGCCGTTGTTCGTATGTTTTTCTCCTTTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.90% 46.00% 0.08% 0.00% NA
All Indica  2759 24.80% 75.10% 0.11% 0.00% NA
All Japonica  1512 98.80% 1.20% 0.00% 0.00% NA
Aus  269 76.20% 23.80% 0.00% 0.00% NA
Indica I  595 20.00% 80.00% 0.00% 0.00% NA
Indica II  465 26.90% 72.90% 0.22% 0.00% NA
Indica III  913 26.70% 73.30% 0.00% 0.00% NA
Indica Intermediate  786 24.90% 74.80% 0.25% 0.00% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 76.70% 22.20% 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
vg0506745303 A -> C LOC_Os05g11820-LOC_Os05g11840 intergenic_region ; MODIFIER silent_mutation Average:52.777; most accessible tissue: Callus, score: 77.655 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506745303 3.87E-06 NA mr1185 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
vg0506745303 NA 9.49E-06 mr1185 Ind_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
vg0506745303 6.08E-06 3.47E-06 mr1269 Ind_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
vg0506745303 NA 5.88E-07 mr1677 Ind_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
vg0506745303 5.82E-07 NA mr1678 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
vg0506745303 3.81E-06 8.18E-08 mr1678 Ind_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
vg0506745303 NA 3.92E-13 mr1514_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