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Detailed information for vg0519883496:

Variant ID: vg0519883496 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 19883496
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


AATCTTCAGCCATAATATAAGATTGCATCCTACTACACCAATGAGAAAAATTCGTTCCATCGAAAACATGAGGCTTAGTTGAGAACCTAGCGGGAGTAGC[C/T]
ATGGCAAAAACTCTAGATCAATAAAAATCCAAAGAGGAAAACAAGGCTCTGATACCACTTGTAGGATTGAATCATAAGAACTAAGCCAACTAGAGGGGGG

Reverse complement sequence

CCCCCCTCTAGTTGGCTTAGTTCTTATGATTCAATCCTACAAGTGGTATCAGAGCCTTGTTTTCCTCTTTGGATTTTTATTGATCTAGAGTTTTTGCCAT[G/A]
GCTACTCCCGCTAGGTTCTCAACTAAGCCTCATGTTTTCGATGGAACGAATTTTTCTCATTGGTGTAGTAGGATGCAATCTTATATTATGGCTGAAGATT

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 98.40% 1.40% 0.23% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.00% 4.20% 0.73% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 93.00% 5.90% 1.17% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 91.30% 7.90% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 0.00% 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
vg0519883496 C -> T LOC_Os05g33750.1 upstream_gene_variant ; 499.0bp to feature; MODIFIER silent_mutation Average:39.808; most accessible tissue: Zhenshan97 flag leaf, score: 53.795 N N N N
vg0519883496 C -> T LOC_Os05g33750-LOC_Os05g33760 intergenic_region ; MODIFIER silent_mutation Average:39.808; most accessible tissue: Zhenshan97 flag leaf, score: 53.795 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0519883496 4.59E-06 NA Grain_length Jap_All YES 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