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Detailed information for vg1224021705:

Variant ID: vg1224021705 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 24021705
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


TTGATCTATATGCTATGGAGAAAACCGTGTGAGAGAAATCACTAAAATTGATGGGAAATCCTGGATTGGAGACATGCCTAATTCGGTTGAGCCGAATCGG[C/T]
CGACTCTTCCGCCTCCCTCGCATCTCTCTGTTTCTCTCTTTCTCTAATGACGCCACGCCGGGAACACGGTGACATAGTCTCAGACTGTTTGGCTGGACTT

Reverse complement sequence

AAGTCCAGCCAAACAGTCTGAGACTATGTCACCGTGTTCCCGGCGTGGCGTCATTAGAGAAAGAGAGAAACAGAGAGATGCGAGGGAGGCGGAAGAGTCG[G/A]
CCGATTCGGCTCAACCGAATTAGGCATGTCTCCAATCCAGGATTTCCCATCAATTTTAGTGATTTCTCTCACACGGTTTTCTCCATAGCATATAGATCAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.00% 12.90% 0.13% 0.00% NA
All Indica  2759 78.80% 21.10% 0.18% 0.00% NA
All Japonica  1512 99.60% 0.30% 0.07% 0.00% NA
Aus  269 95.20% 4.80% 0.00% 0.00% NA
Indica I  595 74.50% 24.90% 0.67% 0.00% NA
Indica II  465 93.30% 6.70% 0.00% 0.00% NA
Indica III  913 81.40% 18.60% 0.00% 0.00% NA
Indica Intermediate  786 70.40% 29.50% 0.13% 0.00% NA
Temperate Japonica  767 99.30% 0.50% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 0.00% 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
vg1224021705 C -> T LOC_Os12g39040-LOC_Os12g39060 intergenic_region ; MODIFIER silent_mutation Average:43.216; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1224021705 8.95E-07 8.97E-07 mr1160 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
vg1224021705 9.42E-07 9.42E-07 mr1160 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
vg1224021705 NA 4.25E-06 mr1193 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
vg1224021705 NA 2.13E-06 mr1950 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
vg1224021705 NA 1.58E-06 mr1655_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
vg1224021705 NA 9.94E-06 mr1726_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