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Detailed information for vg0301215623:

Variant ID: vg0301215623 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 1215623
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.80, T: 0.20, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


TGATGTCTAGGTTTAAATGATTTTCATCAGATGTAGAGGTCACAGCCTTCCACATGCCATTTTTCATTGATATACCCGTGTATCAACACATTAAGCAATA[C/T]
TCTTAGTCTCCAAGTCATGATATTTCTGGCATATCTCTTCTTCTCAGTTTTTTTTAACATAAAGCTTTGTCCATATATATATTGTATAGCATCAAATAGA

Reverse complement sequence

TCTATTTGATGCTATACAATATATATATGGACAAAGCTTTATGTTAAAAAAAACTGAGAAGAAGAGATATGCCAGAAATATCATGACTTGGAGACTAAGA[G/A]
TATTGCTTAATGTGTTGATACACGGGTATATCAATGAAAAATGGCATGTGGAAGGCTGTGACCTCTACATCTGATGAAAATCATTTAAACCTAGACATCA

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 62.50% 37.10% 0.38% 0.00% NA
All Indica  2759 96.90% 3.00% 0.07% 0.00% NA
All Japonica  1512 6.80% 92.50% 0.66% 0.00% NA
Aus  269 21.60% 77.70% 0.74% 0.00% NA
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 94.00% 6.00% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 95.00% 4.70% 0.25% 0.00% NA
Temperate Japonica  767 0.50% 99.10% 0.39% 0.00% NA
Tropical Japonica  504 18.50% 80.80% 0.79% 0.00% NA
Japonica Intermediate  241 2.50% 96.30% 1.24% 0.00% NA
VI/Aromatic  96 75.00% 24.00% 1.04% 0.00% NA
Intermediate  90 52.20% 44.40% 3.33% 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
vg0301215623 C -> T LOC_Os03g02980.2 intron_variant ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301215623 C -> T LOC_Os03g02980.1 intron_variant ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0301215623 NA 6.47E-06 mr1639 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
vg0301215623 1.09E-06 1.09E-06 mr1335_2 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
vg0301215623 NA 8.41E-06 mr1397_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
vg0301215623 NA 4.96E-07 mr1567_2 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
vg0301215623 NA 6.27E-06 mr1646_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
vg0301215623 NA 4.75E-06 mr1738_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