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Detailed information for vg0324677253:

Variant ID: vg0324677253 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24677253
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


GGTATCACCACTATAGGTGCCGGAAGTGCTAAAACCAGCAACTATAGGCTTTTTCCCACCTCCGCGGGTTGAAATCGCAAAAAACAACACCTTTAAGCAA[C/T]
TATAGATGTCGGTTCTAAATAAAAACCGACACCTATTCTTTAAAAAAAATGACACCTATGAATTGAGCCGAGCCGGTGGGCCCCACCACAACGTGTGGAG

Reverse complement sequence

CTCCACACGTTGTGGTGGGGCCCACCGGCTCGGCTCAATTCATAGGTGTCATTTTTTTTAAAGAATAGGTGTCGGTTTTTATTTAGAACCGACATCTATA[G/A]
TTGCTTAAAGGTGTTGTTTTTTGCGATTTCAACCCGCGGAGGTGGGAAAAAGCCTATAGTTGCTGGTTTTAGCACTTCCGGCACCTATAGTGGTGATACC

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 54.50% 45.50% 0.06% 0.00% NA
All Indica  2759 82.60% 17.30% 0.07% 0.00% NA
All Japonica  1512 0.90% 99.10% 0.07% 0.00% NA
Aus  269 87.00% 13.00% 0.00% 0.00% NA
Indica I  595 66.90% 33.10% 0.00% 0.00% NA
Indica II  465 96.80% 3.00% 0.22% 0.00% NA
Indica III  913 90.30% 9.70% 0.00% 0.00% NA
Indica Intermediate  786 77.40% 22.50% 0.13% 0.00% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 98.80% 0.20% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 42.20% 57.80% 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
vg0324677253 C -> T LOC_Os03g43950-LOC_Os03g43960 intergenic_region ; MODIFIER silent_mutation Average:61.273; most accessible tissue: Minghui63 root, score: 75.806 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0324677253 NA 1.59E-06 mr1291 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
vg0324677253 NA 1.54E-08 mr1595 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
vg0324677253 NA 4.32E-09 mr1637 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
vg0324677253 NA 1.98E-08 mr1205_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
vg0324677253 7.41E-06 NA mr1295_2 Ind_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
vg0324677253 NA 5.50E-07 mr1302_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
vg0324677253 NA 6.41E-25 mr1386_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
vg0324677253 NA 1.56E-06 mr1386_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
vg0324677253 NA 1.14E-07 mr1431_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
vg0324677253 NA 8.51E-06 mr1754_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
vg0324677253 NA 6.11E-15 mr1767_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