Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1003336967:

Variant ID: vg1003336967 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3336967
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 51. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTCTCTCCTCGGGAGAAGACTAGAAAACCGAGTTTGCCCGCCGGCACACCAAACACACACTTTTCGGGGTTCAGTTTCATGCGCGTTGACCTAAGGCT[G/A]
TCGAAAGTCTCAGCCAAGTCCTGTAATAACGTCTCCTGGTGGCGCGTCTTTACCACCAGGTCATCGACATACGCCTCTACATTGCGCCTTATTTGATTAC

Reverse complement sequence

GTAATCAAATAAGGCGCAATGTAGAGGCGTATGTCGATGACCTGGTGGTAAAGACGCGCCACCAGGAGACGTTATTACAGGACTTGGCTGAGACTTTCGA[C/T]
AGCCTTAGGTCAACGCGCATGAAACTGAACCCCGAAAAGTGTGTGTTTGGTGTGCCGGCGGGCAAACTCGGTTTTCTAGTCTTCTCCCGAGGAGAGAAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.60% 9.60% 4.00% 23.78% NA
All Indica  2759 39.50% 15.00% 6.34% 39.11% NA
All Japonica  1512 96.90% 2.30% 0.26% 0.53% NA
Aus  269 97.00% 0.00% 0.00% 2.97% NA
Indica I  595 49.10% 16.50% 4.87% 29.58% NA
Indica II  465 47.10% 14.20% 5.16% 33.55% NA
Indica III  913 26.90% 15.80% 8.11% 49.18% NA
Indica Intermediate  786 42.50% 13.50% 6.11% 37.91% NA
Temperate Japonica  767 99.30% 0.00% 0.26% 0.39% NA
Tropical Japonica  504 92.10% 6.70% 0.40% 0.79% NA
Japonica Intermediate  241 99.20% 0.40% 0.00% 0.41% NA
VI/Aromatic  96 75.00% 0.00% 4.17% 20.83% NA
Intermediate  90 77.80% 5.60% 6.67% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1003336967 G -> A LOC_Os10g06490.1 synonymous_variant ; p.Asp592Asp; LOW synonymous_codon Average:29.346; most accessible tissue: Zhenshan97 flag leaf, score: 65.82 N N N N
vg1003336967 G -> DEL LOC_Os10g06490.1 N frameshift_variant Average:29.346; most accessible tissue: Zhenshan97 flag leaf, score: 65.82 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003336967 NA 3.56E-06 mr1538 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
vg1003336967 6.27E-10 4.07E-09 mr1547 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
vg1003336967 2.35E-08 9.50E-10 mr1547 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
vg1003336967 7.79E-15 1.39E-13 mr1709 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
vg1003336967 1.37E-12 3.66E-11 mr1709 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
vg1003336967 NA 4.40E-07 mr1538_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
vg1003336967 3.07E-08 4.38E-09 mr1547_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
vg1003336967 5.13E-09 1.18E-11 mr1547_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
vg1003336967 9.53E-14 2.37E-12 mr1709_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
vg1003336967 2.56E-09 1.96E-10 mr1709_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