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Detailed information for vg0819943568:

Variant ID: vg0819943568 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 19943568
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, A: 0.04, T: 0.02, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:


CACATCATCCTCCCATTCTTCACGGAAAACCGTTCTCGGTTTTTCCATATGGTGTTCTTCATATAGTCCATTCAAAATAACCTGTTTCATCCAATCAAAA[A/C]
TAGAGAAACTCGAAGTAGTGTGATTAGCAATAACATGTTTCTCTAAATTCGAACAAATGAAAACTCTATGCACCAAATATATTCCTCTATCATTATATTT

Reverse complement sequence

AAATATAATGATAGAGGAATATATTTGGTGCATAGAGTTTTCATTTGTTCGAATTTAGAGAAACATGTTATTGCTAATCACACTACTTCGAGTTTCTCTA[T/G]
TTTTGATTGGATGAAACAGGTTATTTTGAATGGACTATATGAAGAACACCATATGGAAAAACCGAGAACGGTTTTCCGTGAAGAATGGGAGGATGATGTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 16.60% 15.30% 27.78% 40.39% NA
All Indica  2759 0.50% 1.60% 38.20% 59.70% NA
All Japonica  1512 48.10% 42.50% 3.44% 5.89% NA
Aus  269 0.70% 1.10% 58.36% 39.78% NA
Indica I  595 1.20% 1.30% 28.91% 68.57% NA
Indica II  465 0.40% 2.40% 38.28% 58.92% NA
Indica III  913 0.10% 0.50% 45.35% 54.00% NA
Indica Intermediate  786 0.40% 2.70% 36.90% 60.05% NA
Temperate Japonica  767 37.90% 60.90% 0.26% 0.91% NA
Tropical Japonica  504 69.60% 9.70% 8.13% 12.50% NA
Japonica Intermediate  241 35.70% 52.70% 3.73% 7.88% NA
VI/Aromatic  96 24.00% 5.20% 29.17% 41.67% NA
Intermediate  90 18.90% 27.80% 24.44% 28.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0819943568 A -> C LOC_Os08g32140.1 missense_variant ; p.Ile430Ser; MODERATE nonsynonymous_codon ; I430S Average:5.207; most accessible tissue: Minghui63 flower, score: 10.335 possibly damaging -1.518 TOLERATED 0.50
vg0819943568 A -> DEL LOC_Os08g32140.1 N frameshift_variant Average:5.207; most accessible tissue: Minghui63 flower, score: 10.335 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0819943568 NA 6.76E-10 mr1282 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
vg0819943568 NA 1.16E-10 mr1790 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
vg0819943568 NA 1.58E-07 mr1805 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
vg0819943568 NA 2.70E-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
vg0819943568 NA 1.11E-12 mr1182_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
vg0819943568 5.46E-06 1.04E-11 mr1228_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
vg0819943568 NA 5.46E-07 mr1228_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
vg0819943568 NA 6.19E-06 mr1262_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
vg0819943568 NA 7.20E-11 mr1282_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
vg0819943568 NA 5.94E-08 mr1376_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
vg0819943568 NA 7.44E-07 mr1379_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
vg0819943568 NA 4.24E-08 mr1431_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
vg0819943568 1.30E-06 NA mr1551_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
vg0819943568 7.51E-06 9.33E-11 mr1551_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
vg0819943568 NA 2.00E-08 mr1606_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
vg0819943568 NA 5.96E-09 mr1681_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
vg0819943568 NA 1.31E-07 mr1765_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
vg0819943568 NA 4.20E-06 mr1869_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
vg0819943568 NA 2.65E-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
vg0819943568 NA 9.89E-09 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
vg0819943568 NA 5.64E-18 mr1980_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