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Detailed information for vg0714511673:

Variant ID: vg0714511673 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 14511673
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.03, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TAAACTAAAAGAGTTTTGTGAAATCTACTCTTCTTTATATGTACCATCGACAAACGCCCACTTCCCAAAGTGCCATCAACAAACACCTCCCTTGTACGCC[A/G]
TGAGAATCTCAAATCACGACATGACGAATGTGCCCCCCACCGCTACCAGCGTTCTAGAAACATTATGCAGGTATTACTCCAAAACAAAGCAAAGAAGCTC

Reverse complement sequence

GAGCTTCTTTGCTTTGTTTTGGAGTAATACCTGCATAATGTTTCTAGAACGCTGGTAGCGGTGGGGGGCACATTCGTCATGTCGTGATTTGAGATTCTCA[T/C]
GGCGTACAAGGGAGGTGTTTGTTGATGGCACTTTGGGAAGTGGGCGTTTGTCGATGGTACATATAAAGAAGAGTAGATTTCACAAAACTCTTTTAGTTTA

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 64.30% 35.50% 0.17% 0.00% NA
All Indica  2759 44.00% 55.70% 0.25% 0.00% NA
All Japonica  1512 98.80% 1.20% 0.00% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 59.20% 40.50% 0.34% 0.00% NA
Indica II  465 19.60% 80.20% 0.22% 0.00% NA
Indica III  913 41.10% 58.80% 0.11% 0.00% NA
Indica Intermediate  786 50.50% 49.10% 0.38% 0.00% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 22.90% 77.10% 0.00% 0.00% NA
Intermediate  90 58.90% 40.00% 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
vg0714511673 A -> G LOC_Os07g25390.1 intron_variant ; MODIFIER silent_mutation Average:66.446; most accessible tissue: Zhenshan97 young leaf, score: 78.044 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0714511673 NA 9.93E-07 mr1212 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
vg0714511673 NA 6.76E-08 mr1354 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
vg0714511673 NA 6.99E-10 mr1705 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
vg0714511673 NA 1.50E-06 mr1761 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
vg0714511673 NA 1.37E-06 mr1293_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
vg0714511673 NA 8.66E-07 mr1294_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
vg0714511673 NA 5.30E-07 mr1428_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
vg0714511673 NA 5.65E-06 mr1497_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