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Detailed information for vg0515318112:

Variant ID: vg0515318112 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 15318112
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTAACCGAGTTTGATCTTCGGTATGAGTCGCCGAAGGCGATTAAGGGACAAGCTATAGCCGATTTTATTGTGGAACATCGTGATGATTCAATCGGCTC[G/A]
GTTGAAATAGTGCCATGGACTTTATTCTTTGATGGATCGGTGTGCACTCATGGTTGTGGTATTGACCTAGTTATAATTTCCCCTAGGGGGGCATGTTTCG

Reverse complement sequence

CGAAACATGCCCCCCTAGGGGAAATTATAACTAGGTCAATACCACAACCATGAGTGCACACCGATCCATCAAAGAATAAAGTCCATGGCACTATTTCAAC[C/T]
GAGCCGATTGAATCATCACGATGTTCCACAATAAAATCGGCTATAGCTTGTCCCTTAATCGCCTTCGGCGACTCATACCGAAGATCAAACTCGGTTAAAG

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 60.90% 39.00% 0.13% 0.00% NA
All Indica  2759 47.90% 52.00% 0.14% 0.00% NA
All Japonica  1512 78.10% 21.80% 0.07% 0.00% NA
Aus  269 81.00% 19.00% 0.00% 0.00% NA
Indica I  595 31.90% 67.90% 0.17% 0.00% NA
Indica II  465 62.60% 37.40% 0.00% 0.00% NA
Indica III  913 55.40% 44.40% 0.22% 0.00% NA
Indica Intermediate  786 42.50% 57.40% 0.13% 0.00% NA
Temperate Japonica  767 94.40% 5.60% 0.00% 0.00% NA
Tropical Japonica  504 52.00% 47.80% 0.20% 0.00% NA
Japonica Intermediate  241 80.90% 19.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 68.90% 30.00% 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
vg0515318112 G -> A LOC_Os05g26330.1 synonymous_variant ; p.Ser358Ser; LOW synonymous_codon Average:35.111; most accessible tissue: Zhenshan97 flag leaf, score: 58.772 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0515318112 NA 8.28E-07 mr1243 Jap_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
vg0515318112 NA 2.49E-13 mr1771 Jap_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
vg0515318112 NA 5.98E-12 mr1784 Jap_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
vg0515318112 NA 1.25E-10 mr1800 Jap_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
vg0515318112 9.92E-06 1.05E-10 mr1862 Jap_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
vg0515318112 NA 9.71E-07 mr1217_2 Jap_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
vg0515318112 NA 7.31E-12 mr1410_2 Jap_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
vg0515318112 NA 1.36E-07 mr1676_2 Jap_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