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Detailed information for vg1002297395:

Variant ID: vg1002297395 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2297395
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


TCACAAGTTTACAGCAGAAAAAAAAGCATAATAATGTATATAGTAAATCACTAAATATGCCCAAACTGAAAATGACCCAAAAATTTGTTGCACACCAAGC[G/A]
GCATTGCAACTACAATATTGTTAGTCTTGCACAGCGATCTAATGCAATGAAAACTGGGAGTGTACTCTAGAAACAGTACGACTTGCCAATGCACCCCCTT

Reverse complement sequence

AAGGGGGTGCATTGGCAAGTCGTACTGTTTCTAGAGTACACTCCCAGTTTTCATTGCATTAGATCGCTGTGCAAGACTAACAATATTGTAGTTGCAATGC[C/T]
GCTTGGTGTGCAACAAATTTTTGGGTCATTTTCAGTTTGGGCATATTTAGTGATTTACTATATACATTATTATGCTTTTTTTTCTGCTGTAAACTTGTGA

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 92.00% 7.60% 0.47% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 77.30% 21.40% 1.32% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 92.80% 5.90% 1.30% 0.00% NA
Tropical Japonica  504 47.40% 50.80% 1.79% 0.00% NA
Japonica Intermediate  241 90.50% 9.10% 0.41% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 88.90% 8.90% 2.22% 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
vg1002297395 G -> A LOC_Os10g04770.1 upstream_gene_variant ; 4627.0bp to feature; MODIFIER silent_mutation Average:60.417; most accessible tissue: Zhenshan97 young leaf, score: 70.625 N N N N
vg1002297395 G -> A LOC_Os10g04780.1 downstream_gene_variant ; 2043.0bp to feature; MODIFIER silent_mutation Average:60.417; most accessible tissue: Zhenshan97 young leaf, score: 70.625 N N N N
vg1002297395 G -> A LOC_Os10g04770-LOC_Os10g04780 intergenic_region ; MODIFIER silent_mutation Average:60.417; most accessible tissue: Zhenshan97 young leaf, score: 70.625 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002297395 NA 3.36E-09 mr1379_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
vg1002297395 NA 6.02E-06 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
vg1002297395 9.49E-08 NA mr1758_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
vg1002297395 NA 1.46E-08 mr1758_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
vg1002297395 NA 1.86E-11 mr1905_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
vg1002297395 NA 1.35E-07 mr1905_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