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Detailed information for vg1100923864:

Variant ID: vg1100923864 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 923864
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.24, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTCTTAACCAGAAGCACTGGGGCTCCCCAAGGGGATGAGCTAGGTCGCACATAACCTTTACTTTCCAACTCTTCGATTTGTCTTTTGACTTCTGCTAA[C/T]
TCATTAGCTGCCATTCGGTAGGGTCTTTTTGCAATTGGTGCAGTGCCTGGTGCTAGTTCTATGGCGAACTGAATCTCTCGGTCTGGTGGCATACTCGTTA

Reverse complement sequence

TAACGAGTATGCCACCAGACCGAGAGATTCAGTTCGCCATAGAACTAGCACCAGGCACTGCACCAATTGCAAAAAGACCCTACCGAATGGCAGCTAATGA[G/A]
TTAGCAGAAGTCAAAAGACAAATCGAAGAGTTGGAAAGTAAAGGTTATGTGCGACCTAGCTCATCCCCTTGGGGAGCCCCAGTGCTTCTGGTTAAGAAAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 44.90% 6.00% 41.37% 7.79% NA
All Indica  2759 12.80% 9.30% 65.24% 12.61% NA
All Japonica  1512 97.90% 0.00% 0.99% 1.06% NA
Aus  269 48.30% 9.30% 42.01% 0.37% NA
Indica I  595 9.20% 0.20% 62.35% 28.24% NA
Indica II  465 21.50% 20.90% 52.26% 5.38% NA
Indica III  913 10.70% 7.10% 75.25% 6.90% NA
Indica Intermediate  786 12.80% 12.00% 63.49% 11.70% NA
Temperate Japonica  767 97.70% 0.00% 0.78% 1.56% NA
Tropical Japonica  504 98.80% 0.00% 0.99% 0.20% NA
Japonica Intermediate  241 97.10% 0.00% 1.66% 1.24% NA
VI/Aromatic  96 92.70% 0.00% 7.29% 0.00% NA
Intermediate  90 73.30% 1.10% 22.22% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1100923864 C -> T LOC_Os11g02780.1 synonymous_variant ; p.Glu894Glu; LOW synonymous_codon Average:25.018; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N
vg1100923864 C -> DEL LOC_Os11g02780.1 N frameshift_variant Average:25.018; most accessible tissue: Minghui63 panicle, score: 64.459 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1100923864 NA 4.20E-06 mr1032 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
vg1100923864 NA 1.07E-06 mr1155 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
vg1100923864 NA 4.85E-06 mr1165 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
vg1100923864 NA 7.42E-07 mr1291 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
vg1100923864 NA 7.82E-07 mr1477 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
vg1100923864 NA 1.57E-06 mr1478 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
vg1100923864 NA 5.19E-06 mr1676 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
vg1100923864 NA 5.37E-10 mr1720 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
vg1100923864 2.36E-06 4.43E-09 mr1720 Ind_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
vg1100923864 NA 4.54E-06 mr1755 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
vg1100923864 NA 1.65E-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