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Detailed information for vg0519883496:

Variant ID: vg0519883496 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 19883496
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary 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 Size	Frequency 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