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Detailed information for vg0403204395:

Variant ID: vg0403204395 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 3204395
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, A: 0.04, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTGGCGGGATGCGTCGCAATAGACTTGGAAGTCTTTCATCTGGTCGGGCAGAATCAAAACTGGTGCGGATACTAATATCTTTTTGAGCTCCTCAAAAC[T/A]
CTTATCGCACTCAGCTGTCCATTTAAACTTCTCATCTTTCTTAAGCAACTGAGTCATGGGTCGGGCGATCCTGGAGAAGTTCTCGATGAATCGGCGGTAA

Reverse complement sequence

TTACCGCCGATTCATCGAGAACTTCTCCAGGATCGCCCGACCCATGACTCAGTTGCTTAAGAAAGATGAGAAGTTTAAATGGACAGCTGAGTGCGATAAG[A/T]
GTTTTGAGGAGCTCAAAAAGATATTAGTATCCGCACCAGTTTTGATTCTGCCCGACCAGATGAAAGACTTCCAAGTCTATTGCGACGCATCCCGCCACGG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.20% 14.60% 4.25% 18.01% NA
All Indica  2759 51.10% 24.10% 5.51% 19.21% NA
All Japonica  1512 78.30% 0.90% 2.25% 18.58% NA
Aus  269 97.80% 0.40% 1.12% 0.74% NA
Indica I  595 42.90% 47.10% 2.02% 8.07% NA
Indica II  465 49.00% 13.80% 7.96% 29.25% NA
Indica III  913 57.20% 14.70% 6.02% 22.12% NA
Indica Intermediate  786 51.70% 23.90% 6.11% 18.32% NA
Temperate Japonica  767 85.80% 0.70% 1.69% 11.86% NA
Tropical Japonica  504 71.60% 0.40% 2.58% 25.40% NA
Japonica Intermediate  241 68.50% 2.50% 3.32% 25.73% NA
VI/Aromatic  96 76.00% 0.00% 5.21% 18.75% NA
Intermediate  90 61.10% 8.90% 7.78% 22.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0403204395 T -> DEL LOC_Os04g06144.1 N frameshift_variant Average:8.771; most accessible tissue: Callus, score: 17.086 N N N N
vg0403204395 T -> A LOC_Os04g06144.1 missense_variant ; p.Ser563Cys; MODERATE nonsynonymous_codon ; S563C Average:8.771; most accessible tissue: Callus, score: 17.086 benign 1.167 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0403204395 NA 1.33E-32 mr1026 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
vg0403204395 NA 1.01E-16 mr1026 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
vg0403204395 NA 1.28E-06 mr1113 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
vg0403204395 NA 1.84E-06 mr1114 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
vg0403204395 NA 4.01E-06 mr1116 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
vg0403204395 NA 2.71E-16 mr1118 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
vg0403204395 NA 9.86E-17 mr1118 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
vg0403204395 NA 5.68E-15 mr1161 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
vg0403204395 3.18E-06 NA mr1495 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
vg0403204395 5.36E-07 1.62E-22 mr1495 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
vg0403204395 NA 6.32E-08 mr1496 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
vg0403204395 NA 6.07E-06 mr1789 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
vg0403204395 NA 1.29E-09 mr1794 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
vg0403204395 NA 5.81E-06 mr1114_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
vg0403204395 NA 1.52E-20 mr1118_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
vg0403204395 NA 1.07E-22 mr1118_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
vg0403204395 NA 7.01E-08 mr1120_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
vg0403204395 6.41E-06 2.36E-35 mr1161_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
vg0403204395 NA 5.24E-19 mr1161_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
vg0403204395 NA 1.95E-06 mr1233_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
vg0403204395 NA 1.25E-06 mr1247_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
vg0403204395 NA 3.09E-28 mr1495_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
vg0403204395 NA 8.19E-24 mr1495_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
vg0403204395 NA 4.96E-08 mr1496_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
vg0403204395 NA 4.76E-06 mr1655_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
vg0403204395 NA 6.80E-14 mr1794_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
vg0403204395 NA 3.11E-07 mr1936_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
vg0403204395 NA 2.69E-06 mr1961_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