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Search for Variation information by Variation ID:

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

Detailed information for vg0301371771:

Variant ID: vg0301371771 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 1371771
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, A: 0.12, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


TCGGGAATGCTTCGCCGAATGCCGGTCGCCACCCGATGATCTCCTTTGCTAGAAGAACGCCGTGCGCCAACATCTCCTTCAGATTATCTTCCGTCACATC[A/G]
GAGGGCGCCCACTGACTCTCGAAGCTTTCTCTTTTTTCCGCCATGAATGTGGACTGGATGGTTTGATTTGGTCCGAGATACGGCTGGAAAGGGATGGGGA

Reverse complement sequence

TCCCCATCCCTTTCCAGCCGTATCTCGGACCAAATCAAACCATCCAGTCCACATTCATGGCGGAAAAAAGAGAAAGCTTCGAGAGTCAGTGGGCGCCCTC[T/C]
GATGTGACGGAAGATAATCTGAAGGAGATGTTGGCGCACGGCGTTCTTCTAGCAAAGGAGATCATCGGGTGGCGACCGGCATTCGGCGAAGCATTCCCGA

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 28.30% 12.00% 9.16% 50.57% NA
All Indica  2759 4.00% 2.40% 11.34% 82.24% NA
All Japonica  1512 67.90% 31.70% 0.20% 0.26% NA
Aus  269 43.50% 0.00% 36.43% 20.07% NA
Indica I  595 9.20% 1.00% 3.53% 86.22% NA
Indica II  465 0.90% 6.90% 9.25% 83.01% NA
Indica III  913 0.70% 1.20% 18.29% 79.85% NA
Indica Intermediate  786 5.90% 2.20% 10.43% 81.55% NA
Temperate Japonica  767 41.70% 57.80% 0.39% 0.13% NA
Tropical Japonica  504 97.20% 2.40% 0.00% 0.40% NA
Japonica Intermediate  241 89.60% 10.00% 0.00% 0.41% NA
VI/Aromatic  96 54.20% 1.00% 11.46% 33.33% NA
Intermediate  90 35.60% 21.10% 8.89% 34.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0301371771 A -> DEL LOC_Os03g03220.1 N frameshift_variant Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301371771 A -> G LOC_Os03g03220.1 synonymous_variant ; p.Ser15Ser; LOW synonymous_codon Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0301371771 NA 4.36E-09 mr1137 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
vg0301371771 NA 1.38E-06 mr1183 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
vg0301371771 NA 1.17E-06 mr1503 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
vg0301371771 NA 3.68E-07 mr1617 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
vg0301371771 NA 5.05E-09 mr1648 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
vg0301371771 NA 7.49E-07 mr1057_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
vg0301371771 NA 5.85E-09 mr1137_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
vg0301371771 2.58E-06 6.49E-06 mr1164_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
vg0301371771 NA 4.71E-07 mr1180_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
vg0301371771 NA 5.32E-10 mr1449_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
vg0301371771 NA 2.44E-15 mr1552_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
vg0301371771 NA 1.49E-06 mr1691_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
vg0301371771 NA 2.54E-06 mr1866_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
vg0301371771 NA 1.33E-17 mr1870_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
vg0301371771 NA 2.92E-06 mr1925_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