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Detailed information for vg0316474025:

Variant ID: vg0316474025 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16474025
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.75, G: 0.25, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


ACCATCTTGTGTGAATGCTTCAACCATTTGCTTCTTGTTTCCTCCATACACTCCGAACACGCCCATTTCCCTTTCACAGTTTGGCCAGAAAAGTTGCCAA[A/G]
GGCCGGATAATTGTTGATGGTACAAAACAGCATCGCATGGAGGTTGAAATACTCTTGTGCATATGCGTCCCATGTTCGTGTGCTCTCATTCCATAGCCTT

Reverse complement sequence

AAGGCTATGGAATGAGAGCACACGAACATGGGACGCATATGCACAAGAGTATTTCAACCTCCATGCGATGCTGTTTTGTACCATCAACAATTATCCGGCC[T/C]
TTGGCAACTTTTCTGGCCAAACTGTGAAAGGGAAATGGGCGTGTTCGGAGTGTATGGAGGAAACAAGAAGCAAATGGTTGAAGCATTCACACAAGATGGT

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 74.90% 12.20% 1.50% 11.36% NA
All Indica  2759 91.70% 3.60% 2.17% 2.54% NA
All Japonica  1512 43.10% 30.20% 0.26% 26.46% NA
Aus  269 75.10% 3.70% 1.12% 20.07% NA
Indica I  595 98.00% 2.00% 0.00% 0.00% NA
Indica II  465 97.80% 0.20% 0.43% 1.51% NA
Indica III  913 87.20% 6.10% 4.82% 1.86% NA
Indica Intermediate  786 88.70% 3.70% 1.78% 5.85% NA
Temperate Japonica  767 53.50% 4.70% 0.13% 41.72% NA
Tropical Japonica  504 29.40% 62.30% 0.40% 7.94% NA
Japonica Intermediate  241 39.00% 44.00% 0.41% 16.60% NA
VI/Aromatic  96 91.70% 4.20% 0.00% 4.17% NA
Intermediate  90 74.40% 11.10% 4.44% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0316474025 A -> DEL LOC_Os03g29020.1 N frameshift_variant Average:42.49; most accessible tissue: Minghui63 flag leaf, score: 66.004 N N N N
vg0316474025 A -> G LOC_Os03g29020.1 missense_variant ; p.Phe452Leu; MODERATE nonsynonymous_codon ; F452L Average:42.49; most accessible tissue: Minghui63 flag leaf, score: 66.004 possibly damaging -1.952 TOLERATED 1.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316474025 NA 2.72E-06 mr1401 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
vg0316474025 NA 7.21E-07 mr1077_2 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
vg0316474025 NA 7.76E-09 mr1084_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
vg0316474025 NA 3.89E-06 mr1206_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
vg0316474025 NA 5.97E-10 mr1220_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
vg0316474025 NA 3.72E-06 mr1220_2 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
vg0316474025 NA 2.57E-07 mr1229_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
vg0316474025 NA 7.16E-06 mr1295_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
vg0316474025 NA 1.98E-07 mr1302_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
vg0316474025 NA 7.34E-06 mr1405_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
vg0316474025 NA 5.46E-08 mr1502_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
vg0316474025 NA 2.46E-07 mr1567_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
vg0316474025 NA 2.79E-06 mr1596_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
vg0316474025 NA 1.41E-06 mr1693_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
vg0316474025 NA 6.01E-06 mr1693_2 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
vg0316474025 2.08E-06 2.08E-06 mr1777_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
vg0316474025 NA 1.34E-08 mr1786_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
vg0316474025 NA 4.02E-06 mr1844_2 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
vg0316474025 NA 7.04E-07 mr1880_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