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Detailed information for vg0321873075:

Variant ID: vg0321873075 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21873075
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, T: 0.12, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


GGGTGCAATTACTCAAGGAAGTTGAAGCCGATACCATTGAAATCATGGGGGATTCTTTGCTAGTAATCAGTCAATTGGCAGAAGAGTATGAATGCAAGAA[C/T]
GATACATTGATGGTTTATAATGAGAAGTGCCAGGAACTAATGAAAGAGTTTCGGCTGGTTACATTAAAGCATGTCTCTTAAGAACAAAATATTAAAGCTA

Reverse complement sequence

TAGCTTTAATATTTTGTTCTTAAGAGACATGCTTTAATGTAACCAGCCGAAACTCTTTCATTAGTTCCTGGCACTTCTCATTATAAACCATCAATGTATC[G/A]
TTCTTGCATTCATACTCTTCTGCCAATTGACTGATTACTAGCAAAGAATCCCCCATGATTTCAATGGTATCGGCTTCAACTTCCTTGAGTAATTGCACCC

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 42.00% 21.10% 5.27% 31.68% NA
All Indica  2759 15.20% 32.00% 5.84% 46.94% NA
All Japonica  1512 98.10% 0.30% 0.00% 1.65% NA
Aus  269 9.30% 0.70% 31.60% 58.36% NA
Indica I  595 19.80% 67.40% 4.54% 8.24% NA
Indica II  465 23.40% 12.70% 6.67% 57.20% NA
Indica III  913 2.70% 28.60% 3.50% 65.17% NA
Indica Intermediate  786 21.40% 20.60% 9.03% 48.98% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 95.20% 0.00% 0.00% 4.76% NA
Japonica Intermediate  241 98.30% 1.20% 0.00% 0.41% NA
VI/Aromatic  96 4.20% 92.70% 1.04% 2.08% NA
Intermediate  90 57.80% 20.00% 2.22% 20.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0321873075 C -> T LOC_Os03g39350.1 synonymous_variant ; p.Asn1232Asn; LOW synonymous_codon Average:33.612; most accessible tissue: Zhenshan97 flag leaf, score: 47.303 N N N N
vg0321873075 C -> DEL LOC_Os03g39350.1 N frameshift_variant Average:33.612; most accessible tissue: Zhenshan97 flag leaf, score: 47.303 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321873075 NA 5.14E-09 mr1275 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
vg0321873075 NA 2.76E-23 mr1383 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
vg0321873075 NA 1.18E-17 mr1529 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
vg0321873075 NA 2.74E-12 mr1579 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
vg0321873075 NA 7.08E-16 mr1636 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
vg0321873075 NA 7.63E-14 mr1641 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
vg0321873075 NA 9.30E-09 mr1750 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
vg0321873075 NA 2.87E-15 mr1909 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
vg0321873075 6.52E-06 NA mr1987 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
vg0321873075 3.75E-08 NA mr1750_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
vg0321873075 NA 8.57E-15 mr1750_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
vg0321873075 5.09E-06 NA mr1987_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