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Detailed information for vg0321208630:

Variant ID: vg0321208630 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 21208630
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GGTTGTTATGACGGTTGTAGCCTATGCGAAATGACCAATATGCCTGCAACCATCATTGGGGAGCGATCAAGAGCGTCCAGGTGTAAGGCCAGCCAGAGCC[A/G]
GCGTCACCAGGGTTCGCAGCAGGCCTCCAAACTTCCCTATGTGGTTGACAGGTGGGTCCCTATGGCGGTTGTGACAGTTATGACGGTTTCCGGGACGGTT

Reverse complement sequence

AACCGTCCCGGAAACCGTCATAACTGTCACAACCGCCATAGGGACCCACCTGTCAACCACATAGGGAAGTTTGGAGGCCTGCTGCGAACCCTGGTGACGC[T/C]
GGCTCTGGCTGGCCTTACACCTGGACGCTCTTGATCGCTCCCCAATGATGGTTGCAGGCATATTGGTCATTTCGCATAGGCTACAACCGTCATAACAACC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.50% 43.00% 0.11% 0.38% NA
All Indica  2759 40.60% 58.70% 0.07% 0.62% NA
All Japonica  1512 98.70% 1.30% 0.00% 0.00% NA
Aus  269 0.70% 98.90% 0.37% 0.00% NA
Indica I  595 25.20% 74.50% 0.00% 0.34% NA
Indica II  465 23.70% 76.10% 0.00% 0.22% NA
Indica III  913 51.50% 47.60% 0.11% 0.77% NA
Indica Intermediate  786 49.60% 49.40% 0.13% 0.89% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 96.80% 3.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 55.60% 41.10% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0321208630 A -> DEL LOC_Os03g38190.1 N frameshift_variant Average:50.045; most accessible tissue: Zhenshan97 young leaf, score: 68.315 N N N N
vg0321208630 A -> G LOC_Os03g38190.1 missense_variant ; p.Gln136Arg; MODERATE nonsynonymous_codon ; Q136R Average:50.045; most accessible tissue: Zhenshan97 young leaf, score: 68.315 unknown unknown TOLERATED 0.20

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0321208630 NA 2.88E-06 mr1028 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
vg0321208630 NA 2.67E-10 mr1232 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
vg0321208630 NA 9.70E-11 mr1307 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
vg0321208630 NA 2.64E-07 mr1453 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
vg0321208630 NA 4.98E-13 mr1641 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
vg0321208630 NA 2.51E-07 mr1646 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
vg0321208630 NA 2.61E-18 mr1653 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
vg0321208630 NA 5.33E-06 mr1653 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
vg0321208630 NA 2.32E-08 mr1806 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
vg0321208630 NA 2.42E-16 mr1114_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
vg0321208630 NA 6.43E-17 mr1146_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
vg0321208630 NA 7.88E-06 mr1153_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
vg0321208630 NA 5.32E-10 mr1232_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
vg0321208630 NA 3.29E-16 mr1557_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
vg0321208630 NA 8.75E-09 mr1909_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
vg0321208630 NA 4.49E-08 mr1921_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