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Detailed information for vg0315011663:

Variant ID: vg0315011663 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 15011663
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTATGAGTAATAAAACAACTCATAACAAAATAAATTACAATTACGTAAATTTTTTGAATAAGACAAATGGTCAAACATGTGAGAAAAAGTCAACGGCGT[C/T]
ATCTATTAAAAAAACGGAGGTAGTATGTTATTCCCTTTTCTGCATCCATGATAGATATTGCCTCTGGTTTTAAATGGACAAATCGGACGTCTGGCATTTC

Reverse complement sequence

GAAATGCCAGACGTCCGATTTGTCCATTTAAAACCAGAGGCAATATCTATCATGGATGCAGAAAAGGGAATAACATACTACCTCCGTTTTTTTAATAGAT[G/A]
ACGCCGTTGACTTTTTCTCACATGTTTGACCATTTGTCTTATTCAAAAAATTTACGTAATTGTAATTTATTTTGTTATGAGTTGTTTTATTACTCATAAT

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 51.40% 47.80% 0.78% 0.00% NA
All Indica  2759 31.50% 67.30% 1.12% 0.00% NA
All Japonica  1512 78.00% 22.00% 0.07% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 56.00% 42.40% 1.68% 0.00% NA
Indica II  465 52.90% 45.20% 1.94% 0.00% NA
Indica III  913 12.40% 87.50% 0.11% 0.00% NA
Indica Intermediate  786 22.60% 76.00% 1.40% 0.00% NA
Temperate Japonica  767 96.10% 3.90% 0.00% 0.00% NA
Tropical Japonica  504 51.40% 48.40% 0.20% 0.00% NA
Japonica Intermediate  241 75.90% 24.10% 0.00% 0.00% NA
VI/Aromatic  96 63.50% 36.50% 0.00% 0.00% NA
Intermediate  90 60.00% 34.40% 5.56% 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
vg0315011663 C -> T LOC_Os03g26240.1 upstream_gene_variant ; 2210.0bp to feature; MODIFIER silent_mutation Average:39.111; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg0315011663 C -> T LOC_Os03g26260.1 upstream_gene_variant ; 4143.0bp to feature; MODIFIER silent_mutation Average:39.111; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg0315011663 C -> T LOC_Os03g26229.1 downstream_gene_variant ; 3403.0bp to feature; MODIFIER silent_mutation Average:39.111; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N
vg0315011663 C -> T LOC_Os03g26250.1 intron_variant ; MODIFIER silent_mutation Average:39.111; most accessible tissue: Minghui63 panicle, score: 62.157 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0315011663 NA 1.26E-14 Grain_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0315011663 NA 7.94E-07 mr1088 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
vg0315011663 NA 2.84E-06 mr1104 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
vg0315011663 NA 1.50E-06 mr1179 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
vg0315011663 NA 8.12E-06 mr1213 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
vg0315011663 NA 5.59E-06 mr1236 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
vg0315011663 NA 3.36E-06 mr1502 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
vg0315011663 NA 3.06E-07 mr1620 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
vg0315011663 NA 8.42E-13 mr1769 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
vg0315011663 NA 2.38E-07 mr1422_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
vg0315011663 NA 7.00E-12 mr1533_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
vg0315011663 NA 2.50E-06 mr1583_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