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Detailed information for vg0327912257:

Variant ID: vg0327912257 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 27912257
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


AATATTTGCAGATTTCTATCAGCTTGCTTGTGCATTTGATGGATACTTGTGATTCAATTAATGCGTGCTGAATTTTGTTTTCTTTCAGTTGTTTCAGAAA[T/C]
CTGAGTACCTAAGGTTGGTCCATGATGCACCGAAATATGAAGGCAAGCTCTGTAAGAAGGCTTGCTTGTTAGCATACAAAGAGATCTTGAAGAACGAGAT

Reverse complement sequence

ATCTCGTTCTTCAAGATCTCTTTGTATGCTAACAAGCAAGCCTTCTTACAGAGCTTGCCTTCATATTTCGGTGCATCATGGACCAACCTTAGGTACTCAG[A/G]
TTTCTGAAACAACTGAAAGAAAACAAAATTCAGCACGCATTAATTGAATCACAAGTATCCATCAAATGCACAAGCAAGCTGATAGAAATCTGCAAATATT

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 93.70% 5.80% 0.57% 0.00% NA
All Indica  2759 89.50% 9.60% 0.91% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.50% 2.70% 0.84% 0.00% NA
Indica II  465 76.80% 21.70% 1.51% 0.00% NA
Indica III  913 88.70% 11.00% 0.33% 0.00% NA
Indica Intermediate  786 92.70% 6.00% 1.27% 0.00% NA
Temperate Japonica  767 99.60% 0.30% 0.13% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 94.40% 4.40% 1.11% 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
vg0327912257 T -> C LOC_Os03g49000.1 missense_variant ; p.Ser404Pro; MODERATE nonsynonymous_codon ; S404P Average:34.578; most accessible tissue: Callus, score: 62.642 unknown unknown TOLERATED 0.22

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0327912257 NA 1.90E-09 mr1039 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
vg0327912257 NA 2.19E-06 mr1044 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
vg0327912257 NA 4.80E-09 mr1044 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
vg0327912257 NA 6.68E-06 mr1069 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
vg0327912257 NA 3.88E-07 mr1077 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
vg0327912257 NA 8.19E-06 mr1202 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
vg0327912257 NA 2.11E-06 mr1295 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
vg0327912257 NA 1.73E-06 mr1441 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
vg0327912257 NA 9.81E-07 mr1482 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
vg0327912257 NA 3.11E-09 mr1482 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
vg0327912257 NA 8.31E-06 mr1806 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