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Detailed information for vg0301284105:

Variant ID: vg0301284105 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 1284105
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: 272. )

Flanking Sequence (100 bp) in Reference Genome:


ATCGGCTGAAGGACCGACATCATAAAATCCAAACGATTAGATAAATAGTGAAACCTTTGTTGCAATTGGCTAAATCCAACTTGTGTGTAATCCTTATAAG[C/T]
CGATACAACGTCCAGATAACTCATCAGCTGAAACCCTGATGAAACCCTTGTTGACAATCAAAGGTAGGTTAGTTTTTATGGTTCTAAGCACGACTAAGGT

Reverse complement sequence

ACCTTAGTCGTGCTTAGAACCATAAAAACTAACCTACCTTTGATTGTCAACAAGGGTTTCATCAGGGTTTCAGCTGATGAGTTATCTGGACGTTGTATCG[G/A]
CTTATAAGGATTACACACAAGTTGGATTTAGCCAATTGCAACAAAGGTTTCACTATTTATCTAATCGTTTGGATTTTATGATGTCGGTCCTTCAGCCGAT

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 74.60% 25.30% 0.04% 0.00% NA
All Indica  2759 88.30% 11.70% 0.00% 0.00% NA
All Japonica  1512 46.60% 53.30% 0.13% 0.00% NA
Aus  269 80.70% 19.30% 0.00% 0.00% NA
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 65.80% 34.20% 0.00% 0.00% NA
Indica III  913 96.90% 3.10% 0.00% 0.00% NA
Indica Intermediate  786 84.10% 15.90% 0.00% 0.00% NA
Temperate Japonica  767 59.60% 40.30% 0.13% 0.00% NA
Tropical Japonica  504 41.50% 58.50% 0.00% 0.00% NA
Japonica Intermediate  241 15.80% 83.80% 0.41% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 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
vg0301284105 C -> T LOC_Os03g03080-LOC_Os03g03100 intergenic_region ; 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
vg0301284105 NA 1.01E-06 mr1944 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
vg0301284105 NA 5.49E-06 mr1232_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
vg0301284105 5.35E-07 NA mr1238_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
vg0301284105 6.57E-06 NA mr1484_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
vg0301284105 NA 7.43E-08 mr1557_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
vg0301284105 NA 1.73E-09 mr1566_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
vg0301284105 7.15E-06 NA mr1609_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
vg0301284105 NA 8.90E-06 mr1609_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
vg0301284105 1.44E-06 NA mr1841_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
vg0301284105 7.18E-07 NA mr1900_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