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Detailed information for vg1123404382:

Variant ID: vg1123404382 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23404382
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGGACAGGGCAATCAAGGGAGAATCTCTCAAGCTCTTTGAACCCTTCTTTCTCAATCACTATTGGATTTTCAGGAATGAACTCCAAGCCTAGTACCAGG[C/T]
GCTGTAATTTGATCAAGCCCGCGAGGATCTTGACATCATCTGCCACTTGTTTGCAGACCGTGATCTGCAAGAAAGTAAGACGGTCGAGCCTTTCGATCCA

Reverse complement sequence

TGGATCGAAAGGCTCGACCGTCTTACTTTCTTGCAGATCACGGTCTGCAAACAAGTGGCAGATGATGTCAAGATCCTCGCGGGCTTGATCAAATTACAGC[G/A]
CCTGGTACTAGGCTTGGAGTTCATTCCTGAAAATCCAATAGTGATTGAGAAAGAAGGGTTCAAAGAGCTTGAGAGATTCTCCCTTGATTGCCCTGTCCCA

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 60.60% 39.40% 0.04% 0.00% NA
All Indica  2759 63.40% 36.50% 0.04% 0.00% NA
All Japonica  1512 63.40% 36.60% 0.00% 0.00% NA
Aus  269 7.40% 92.60% 0.00% 0.00% NA
Indica I  595 32.90% 67.10% 0.00% 0.00% NA
Indica II  465 94.80% 4.90% 0.22% 0.00% NA
Indica III  913 72.40% 27.60% 0.00% 0.00% NA
Indica Intermediate  786 57.50% 42.50% 0.00% 0.00% NA
Temperate Japonica  767 78.50% 21.50% 0.00% 0.00% NA
Tropical Japonica  504 38.10% 61.90% 0.00% 0.00% NA
Japonica Intermediate  241 68.50% 31.50% 0.00% 0.00% NA
VI/Aromatic  96 77.10% 22.90% 0.00% 0.00% NA
Intermediate  90 65.60% 33.30% 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
vg1123404382 C -> T LOC_Os11g39310.1 missense_variant ; p.Arg817His; MODERATE nonsynonymous_codon ; R817H Average:58.686; most accessible tissue: Zhenshan97 flower, score: 82.718 benign 0.433 TOLERATED 0.55

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1123404382 NA 8.62E-09 mr1557 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
vg1123404382 NA 1.20E-07 mr1829 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
vg1123404382 NA 1.84E-09 mr1942 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
vg1123404382 NA 8.23E-06 mr1201_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
vg1123404382 NA 6.78E-06 mr1232_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
vg1123404382 NA 4.45E-13 mr1557_2 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
vg1123404382 NA 3.84E-14 mr1598_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
vg1123404382 NA 1.73E-06 mr1619_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
vg1123404382 NA 8.28E-06 mr1795_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
vg1123404382 NA 2.09E-09 mr1829_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
vg1123404382 NA 3.18E-10 mr1962_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