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

Detailed information for vg0910096975:

Variant ID: vg0910096975 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 10096975
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


TCTCCCGACAAAGAAACCAGCCATACCAGCGCCACCGACCTTCCAGAATATGGCTGACAAGAGTCACAAGACCCTCCATGAATTTGTTGCTCCCTCAGCT[G/A]
ACAACGTGGCCATTGGGCCGCAGATCAACCTGGGAGAAGTGGATTTCGATCTGAAGTCCAGCCTCATCACGATGGCGCAGGCTAGCCTGTTCTGCGACAA

Reverse complement sequence

TTGTCGCAGAACAGGCTAGCCTGCGCCATCGTGATGAGGCTGGACTTCAGATCGAAATCCACTTCTCCCAGGTTGATCTGCGGCCCAATGGCCACGTTGT[C/T]
AGCTGAGGGAGCAACAAATTCATGGAGGGTCTTGTGACTCTTGTCAGCCATATTCTGGAAGGTCGGTGGCGCTGGTATGGCTGGTTTCTTTGTCGGGAGA

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 49.60% 39.90% 0.42% 10.16% NA
All Indica  2759 32.50% 66.00% 0.22% 1.23% NA
All Japonica  1512 72.00% 0.60% 0.79% 26.59% NA
Aus  269 89.60% 8.60% 0.00% 1.86% NA
Indica I  595 15.30% 80.80% 0.00% 3.87% NA
Indica II  465 35.10% 64.50% 0.00% 0.43% NA
Indica III  913 39.50% 60.20% 0.00% 0.22% NA
Indica Intermediate  786 36.00% 62.30% 0.76% 0.89% NA
Temperate Japonica  767 98.30% 0.40% 0.26% 1.04% NA
Tropical Japonica  504 26.00% 0.60% 1.39% 72.02% NA
Japonica Intermediate  241 84.60% 1.20% 1.24% 12.86% NA
VI/Aromatic  96 74.00% 3.10% 0.00% 22.92% NA
Intermediate  90 47.80% 31.10% 2.22% 18.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0910096975 G -> DEL LOC_Os09g16480.1 N frameshift_variant Average:52.561; most accessible tissue: Zhenshan97 young leaf, score: 69.723 N N N N
vg0910096975 G -> A LOC_Os09g16480.1 missense_variant ; p.Asp18Asn; MODERATE nonsynonymous_codon ; D18N Average:52.561; most accessible tissue: Zhenshan97 young leaf, score: 69.723 unknown unknown TOLERATED 0.18

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0910096975 NA 7.34E-06 mr1188 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
vg0910096975 2.10E-06 1.41E-06 mr1215 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
vg0910096975 NA 3.43E-07 mr1304 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
vg0910096975 NA 5.24E-06 mr1382 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
vg0910096975 NA 9.46E-08 mr1401 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
vg0910096975 NA 9.52E-06 mr1414 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
vg0910096975 NA 9.68E-06 mr1653 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
vg0910096975 NA 5.34E-07 mr1830 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
vg0910096975 NA 1.18E-08 mr1498_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
vg0910096975 NA 6.57E-06 mr1498_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
vg0910096975 NA 1.70E-08 mr1925_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