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Detailed information for vg0308557129:

Variant ID: vg0308557129 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 8557129
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: 120. )

Flanking Sequence (100 bp) in Reference Genome:


CAGACTTTTTTATCGATAAACTGTAAAAAGAAAAAACTCAAACTAGTGTTAGTCTGTTAGATATGGGTCCTTCTCAGGTTTCCCTTACCGTCGGTAACCG[C/T]
GGGGTACGATAATGGTTACTAGCGGTAGAGTTTGGGGAATTTTTTTACCAAATTCAAAGTTTTTTTAAAAAAACATGAATGTAGTTCTTGATTTTTAGTG

Reverse complement sequence

CACTAAAAATCAAGAACTACATTCATGTTTTTTTAAAAAAACTTTGAATTTGGTAAAAAAATTCCCCAAACTCTACCGCTAGTAACCATTATCGTACCCC[G/A]
CGGTTACCGACGGTAAGGGAAACCTGAGAAGGACCCATATCTAACAGACTAACACTAGTTTGAGTTTTTTCTTTTTACAGTTTATCGATAAAAAAGTCTG

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 63.60% 36.30% 0.04% 0.00% NA
All Indica  2759 39.40% 60.50% 0.07% 0.00% NA
All Japonica  1512 98.70% 1.30% 0.00% 0.00% NA
Aus  269 97.00% 3.00% 0.00% 0.00% NA
Indica I  595 2.20% 97.80% 0.00% 0.00% NA
Indica II  465 26.70% 72.90% 0.43% 0.00% NA
Indica III  913 66.20% 33.80% 0.00% 0.00% NA
Indica Intermediate  786 44.10% 55.90% 0.00% 0.00% NA
Temperate Japonica  767 97.80% 2.20% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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% 23.30% 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
vg0308557129 C -> T LOC_Os03g15550.1 upstream_gene_variant ; 1616.0bp to feature; MODIFIER silent_mutation Average:44.695; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg0308557129 C -> T LOC_Os03g15540-LOC_Os03g15550 intergenic_region ; MODIFIER silent_mutation Average:44.695; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0308557129 NA 1.83E-11 mr1609 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
vg0308557129 NA 5.26E-23 mr1609_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
vg0308557129 NA 4.32E-08 mr1612_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
vg0308557129 NA 7.26E-13 mr1770_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
vg0308557129 NA 9.79E-06 mr1901_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