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Detailed information for vg1216527792:

Variant ID: vg1216527792 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 16527792
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


GGAGCAAGGCTTCCGAGGAAATGATTGCTGCCATCAGGGCAACCACCGCCATCCTCAAGGTTGCATCATCTCCAACACCCATGGCACCACCTCCTCCAGC[A/G]
CCCACCAATTGTTTGATAGAATGCCCCAACAACAACATCAATTGGGTGACGACGAATTCAAGTCACATTGGTGAGGTGCTTGTTCCGACAGCTGACCAGG

Reverse complement sequence

CCTGGTCAGCTGTCGGAACAAGCACCTCACCAATGTGACTTGAATTCGTCGTCACCCAATTGATGTTGTTGTTGGGGCATTCTATCAAACAATTGGTGGG[T/C]
GCTGGAGGAGGTGGTGCCATGGGTGTTGGAGATGATGCAACCTTGAGGATGGCGGTGGTTGCCCTGATGGCAGCAATCATTTCCTCGGAAGCCTTGCTCC

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 42.60% 18.50% 0.74% 38.19% NA
All Indica  2759 48.00% 2.30% 0.80% 48.89% NA
All Japonica  1512 29.80% 51.90% 0.60% 17.66% NA
Aus  269 48.00% 0.00% 0.00% 52.04% NA
Indica I  595 35.50% 1.50% 0.34% 62.69% NA
Indica II  465 19.80% 3.70% 1.08% 75.48% NA
Indica III  913 76.60% 0.90% 0.44% 22.12% NA
Indica Intermediate  786 41.10% 3.70% 1.40% 53.82% NA
Temperate Japonica  767 19.30% 79.70% 0.00% 1.04% NA
Tropical Japonica  504 38.10% 12.70% 1.59% 47.62% NA
Japonica Intermediate  241 46.10% 45.60% 0.41% 7.88% NA
VI/Aromatic  96 75.00% 1.00% 2.08% 21.88% NA
Intermediate  90 41.10% 25.60% 2.22% 31.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1216527792 A -> DEL LOC_Os12g28020.1 N frameshift_variant Average:16.386; most accessible tissue: Callus, score: 54.832 N N N N
vg1216527792 A -> G LOC_Os12g28020.1 synonymous_variant ; p.Ala7Ala; LOW synonymous_codon Average:16.386; most accessible tissue: Callus, score: 54.832 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1216527792 NA 1.10E-06 mr1163 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
vg1216527792 NA 8.75E-07 mr1271 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
vg1216527792 NA 3.43E-06 mr1401 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
vg1216527792 NA 1.88E-06 mr1577 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
vg1216527792 NA 9.30E-07 mr1587 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
vg1216527792 NA 2.69E-07 mr1011_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
vg1216527792 NA 5.01E-06 mr1129_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
vg1216527792 1.52E-06 1.51E-06 mr1162_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
vg1216527792 NA 1.46E-06 mr1257_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
vg1216527792 NA 1.80E-06 mr1629_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
vg1216527792 NA 3.39E-07 mr1653_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
vg1216527792 NA 2.58E-07 mr1749_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
vg1216527792 NA 2.45E-07 mr1754_2 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
vg1216527792 5.19E-08 5.19E-08 mr1754_2 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
vg1216527792 NA 1.45E-08 mr1805_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
vg1216527792 NA 6.20E-09 mr1821_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