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Detailed information for vg1220952777:

Variant ID: vg1220952777 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 20952777
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTATTAAAAAGGAGTAAAAGTTACAAGAAAAACACCATAATGCACCAAAGTACATGACCACACACCACGCGCTACCACCCAAGCACAAACCACTGAGAGT[G/C]
GAGCCTAGCACCAAACAACCCCCGGTAAGCGTGACTGAAGAACACAGCTAGGCCTACGACAACACCACAGAGACGATACTTCAAAAATGATACCACCACA

Reverse complement sequence

TGTGGTGGTATCATTTTTGAAGTATCGTCTCTGTGGTGTTGTCGTAGGCCTAGCTGTGTTCTTCAGTCACGCTTACCGGGGGTTGTTTGGTGCTAGGCTC[C/G]
ACTCTCAGTGGTTTGTGCTTGGGTGGTAGCGCGTGGTGTGTGGTCATGTACTTTGGTGCATTATGGTGTTTTTCTTGTAACTTTTACTCCTTTTTAATAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.00% 39.60% 0.32% 3.00% NA
All Indica  2759 53.20% 46.30% 0.33% 0.18% NA
All Japonica  1512 59.80% 32.50% 0.26% 7.41% NA
Aus  269 91.80% 2.20% 0.00% 5.95% NA
Indica I  595 24.50% 75.00% 0.50% 0.00% NA
Indica II  465 57.40% 42.40% 0.00% 0.22% NA
Indica III  913 66.80% 32.40% 0.55% 0.22% NA
Indica Intermediate  786 56.50% 43.10% 0.13% 0.25% NA
Temperate Japonica  767 89.30% 6.10% 0.26% 4.30% NA
Tropical Japonica  504 14.10% 76.40% 0.40% 9.13% NA
Japonica Intermediate  241 61.40% 24.90% 0.00% 13.69% NA
VI/Aromatic  96 28.10% 65.60% 1.04% 5.21% NA
Intermediate  90 56.70% 37.80% 1.11% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1220952777 G -> C LOC_Os12g34560-LOC_Os12g34580 intergenic_region ; MODIFIER silent_mutation Average:41.406; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg1220952777 G -> DEL N N silent_mutation Average:41.406; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1220952777 NA 4.96E-06 mr1087 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
vg1220952777 NA 1.86E-07 mr1090 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
vg1220952777 NA 3.05E-10 mr1093 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
vg1220952777 NA 4.73E-08 mr1094 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
vg1220952777 NA 2.42E-08 mr1096 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
vg1220952777 NA 2.35E-08 mr1121 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
vg1220952777 NA 1.91E-06 mr1257 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
vg1220952777 5.07E-06 NA mr1334 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
vg1220952777 5.24E-09 1.30E-22 mr1334 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
vg1220952777 NA 2.11E-08 mr1423 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
vg1220952777 NA 4.49E-08 mr1599 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
vg1220952777 NA 3.17E-06 mr1603 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
vg1220952777 NA 1.39E-06 mr1798 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
vg1220952777 NA 3.42E-06 mr1842 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
vg1220952777 6.29E-07 NA mr1334_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
vg1220952777 8.56E-07 5.86E-24 mr1334_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
vg1220952777 8.91E-06 8.89E-06 mr1525_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
vg1220952777 NA 1.35E-07 mr1817_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
vg1220952777 7.00E-06 6.51E-13 mr1991_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