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Detailed information for vg0307865773:

Variant ID: vg0307865773 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 7865773
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGATCCAAGAGAGAAATTTCCTTGGATCACGGAACAGGTCTGGGAGGAATTCCATGTGAAGAAGTCGACCCCCGAGTCCAGAGCTAGTAGCGAGGCATAT[C/T]
GCTTGCTCTAGACCAAGAACCAGCATCCGCATCGGTTTGGCACCGCTGAATATGCCGGTAAGAAAGAGGAATGGCAGCGTGAGGATGAAGAAGCGGAGGA

Reverse complement sequence

TCCTCCGCTTCTTCATCCTCACGCTGCCATTCCTCTTTCTTACCGGCATATTCAGCGGTGCCAAACCGATGCGGATGCTGGTTCTTGGTCTAGAGCAAGC[G/A]
ATATGCCTCGCTACTAGCTCTGGACTCGGGGGTCGACTTCTTCACATGGAATTCCTCCCAGACCTGTTCCGTGATCCAAGGAAATTTCTCTCTTGGATCT

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 90.70% 9.00% 0.28% 0.00% NA
All Indica  2759 93.60% 6.10% 0.29% 0.00% NA
All Japonica  1512 99.00% 1.00% 0.00% 0.00% NA
Aus  269 19.00% 79.20% 1.86% 0.00% NA
Indica I  595 92.30% 7.40% 0.34% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 96.60% 3.40% 0.00% 0.00% NA
Indica Intermediate  786 88.20% 11.10% 0.76% 0.00% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 77.10% 22.90% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0307865773 C -> T LOC_Os03g14480.1 upstream_gene_variant ; 995.0bp to feature; MODIFIER silent_mutation Average:29.873; most accessible tissue: Callus, score: 43.216 N N N N
vg0307865773 C -> T LOC_Os03g14470.1 downstream_gene_variant ; 3188.0bp to feature; MODIFIER silent_mutation Average:29.873; most accessible tissue: Callus, score: 43.216 N N N N
vg0307865773 C -> T LOC_Os03g14490.1 intron_variant ; MODIFIER silent_mutation Average:29.873; most accessible tissue: Callus, score: 43.216 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0307865773 NA 5.86E-07 mr1365 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
vg0307865773 NA 1.11E-06 mr1574 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
vg0307865773 NA 3.11E-11 mr1730 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
vg0307865773 3.72E-06 2.64E-06 mr1263_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
vg0307865773 NA 4.65E-18 mr1874_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