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Detailed information for vg0305233552:

Variant ID: vg0305233552 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 5233552
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, T: 0.05, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


TTGATTGGAAAATAATAGAAAAATTTAAAGAAGCCTCCCCACAATTAAAGAAGGAATTAAAGGAAGAAATACTTAAAGAATTAAAACAAGAAATGGATCA[T/G]
AAATTTGAACAAATAAAAAAGGCAGTAGATGAGAAATTAGAAGTTTCTTTTTCTAATCTGGACACTATGGATCTTGGTGGTCATGGGCAACCAGATGAAT

Reverse complement sequence

ATTCATCTGGTTGCCCATGACCACCAAGATCCATAGTGTCCAGATTAGAAAAAGAAACTTCTAATTTCTCATCTACTGCCTTTTTTATTTGTTCAAATTT[A/C]
TGATCCATTTCTTGTTTTAATTCTTTAAGTATTTCTTCCTTTAATTCCTTCTTTAATTGTGGGGAGGCTTCTTTAAATTTTTCTATTATTTTCCAATCAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 37.20% 17.30% 24.93% 20.57% NA
All Indica  2759 4.40% 21.20% 39.98% 34.40% NA
All Japonica  1512 99.50% 0.10% 0.33% 0.00% NA
Aus  269 1.10% 81.00% 11.90% 5.95% NA
Indica I  595 4.90% 8.60% 43.19% 43.36% NA
Indica II  465 7.50% 7.70% 38.71% 46.02% NA
Indica III  913 2.40% 37.70% 38.23% 21.69% NA
Indica Intermediate  786 4.60% 19.60% 40.33% 35.50% NA
Temperate Japonica  767 99.60% 0.10% 0.26% 0.00% NA
Tropical Japonica  504 99.40% 0.20% 0.40% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 74.00% 7.30% 18.75% 0.00% NA
Intermediate  90 62.20% 7.80% 22.22% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0305233552 T -> DEL LOC_Os03g10270.1 N frameshift_variant Average:9.199; most accessible tissue: Zhenshan97 flower, score: 17.42 N N N N
vg0305233552 T -> G LOC_Os03g10270.1 missense_variant ; p.His164Gln; MODERATE nonsynonymous_codon ; H164Q Average:9.199; most accessible tissue: Zhenshan97 flower, score: 17.42 probably damaging -2.213 TOLERATED 0.79

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0305233552 NA 3.09E-10 Grain_weight All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0305233552 NA 1.25E-06 mr1082 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
vg0305233552 NA 3.22E-32 mr1333 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
vg0305233552 NA 8.79E-08 mr1410 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
vg0305233552 3.80E-07 1.46E-23 mr1518 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
vg0305233552 9.59E-07 6.81E-10 mr1518 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
vg0305233552 NA 3.82E-41 mr1645 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
vg0305233552 NA 1.42E-32 mr1647 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
vg0305233552 3.70E-07 3.62E-25 mr1676 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
vg0305233552 5.00E-07 1.66E-11 mr1676 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
vg0305233552 NA 3.43E-36 mr1682 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
vg0305233552 NA 2.03E-28 mr1686 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
vg0305233552 NA 2.02E-20 mr1754 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
vg0305233552 NA 3.23E-13 mr1874 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
vg0305233552 NA 1.36E-34 mr1181_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
vg0305233552 NA 3.57E-06 mr1181_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
vg0305233552 NA 2.47E-24 mr1233_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
vg0305233552 NA 2.24E-08 mr1299_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
vg0305233552 NA 1.22E-16 mr1342_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
vg0305233552 NA 3.29E-16 mr1416_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
vg0305233552 NA 6.79E-11 mr1537_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
vg0305233552 NA 1.61E-36 mr1541_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
vg0305233552 NA 7.27E-19 mr1657_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
vg0305233552 4.45E-08 2.77E-28 mr1676_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
vg0305233552 1.53E-09 7.17E-16 mr1676_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
vg0305233552 NA 5.23E-08 mr1700_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
vg0305233552 NA 3.48E-06 mr1768_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
vg0305233552 NA 1.90E-18 mr1874_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
vg0305233552 NA 3.69E-30 mr1891_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
vg0305233552 NA 3.11E-23 mr1949_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