Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1005598877:

Variant ID: vg1005598877 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 5598877
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.68, A: 0.32, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GCAAACTTTTTAGCTAGCTTAAAACGATTTCTCACCTAAATTATTTCTCCAATCTACAACCCATATACCGTTGTATTCGTGGTAATTAAACCTTTACAAG[G/A]
AGATATCACATGATTATATTCTGATGAAAGAAAAACTTATGTTCAATTGTTGAAATTCAATGTTTCATACGTGATGGTTAAATGTTTCGACAGGTGTTTC

Reverse complement sequence

GAAACACCTGTCGAAACATTTAACCATCACGTATGAAACATTGAATTTCAACAATTGAACATAAGTTTTTCTTTCATCAGAATATAATCATGTGATATCT[C/T]
CTTGTAAAGGTTTAATTACCACGAATACAACGGTATATGGGTTGTAGATTGGAGAAATAATTTAGGTGAGAAATCGTTTTAAGCTAGCTAAAAAGTTTGC

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 79.60% 20.40% 0.02% 0.00% NA
All Indica  2759 71.40% 28.60% 0.00% 0.00% NA
All Japonica  1512 92.50% 7.50% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 90.90% 9.10% 0.00% 0.00% NA
Indica II  465 70.10% 29.90% 0.00% 0.00% NA
Indica III  913 64.70% 35.30% 0.00% 0.00% NA
Indica Intermediate  786 65.10% 34.90% 0.00% 0.00% NA
Temperate Japonica  767 87.00% 13.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 95.40% 4.60% 0.00% 0.00% NA
VI/Aromatic  96 56.20% 43.80% 0.00% 0.00% NA
Intermediate  90 80.00% 18.90% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1005598877 G -> A LOC_Os10g10180.1 downstream_gene_variant ; 3170.0bp to feature; MODIFIER silent_mutation Average:55.588; most accessible tissue: Minghui63 flag leaf, score: 76.453 N N N N
vg1005598877 G -> A LOC_Os10g10180.3 downstream_gene_variant ; 3170.0bp to feature; MODIFIER silent_mutation Average:55.588; most accessible tissue: Minghui63 flag leaf, score: 76.453 N N N N
vg1005598877 G -> A LOC_Os10g10190.1 intron_variant ; MODIFIER silent_mutation Average:55.588; most accessible tissue: Minghui63 flag leaf, score: 76.453 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1005598877 1.55E-06 9.99E-10 mr1210 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
vg1005598877 1.07E-06 9.26E-10 mr1305 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
vg1005598877 7.70E-08 1.09E-12 mr1585 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
vg1005598877 2.50E-06 2.07E-09 mr1586 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
vg1005598877 NA 7.76E-07 mr1709 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
vg1005598877 NA 4.90E-06 mr1922 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
vg1005598877 4.89E-06 1.14E-11 mr1027_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
vg1005598877 NA 1.42E-06 mr1057_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
vg1005598877 2.19E-07 1.06E-09 mr1305_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
vg1005598877 NA 6.37E-10 mr1580_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
vg1005598877 2.09E-08 1.09E-12 mr1585_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
vg1005598877 NA 5.96E-06 mr1662_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
vg1005598877 NA 5.30E-08 mr1709_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
vg1005598877 6.27E-06 5.99E-11 mr1825_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
vg1005598877 NA 2.98E-06 mr1943_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