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Detailed information for vg0719821103:

Variant ID: vg0719821103 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 19821103
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTGAGAAAATTTCAGGAAAGCCTATTCACCCCCCCCCCTCTAGGCAACATCTCTGCACGTTCATCGCAGGATTGAGAAAACGTAAGAATAGGATAAAC[A/G]
TAGAATTTTGATAGGAATGTAAGTGTAAAACAGAGGATTGCAAAATGCAGGAAAAACACAAGAATGACCGTTTGATTGAACCGCAGGAAAAACACAGGAA

Reverse complement sequence

TTCCTGTGTTTTTCCTGCGGTTCAATCAAACGGTCATTCTTGTGTTTTTCCTGCATTTTGCAATCCTCTGTTTTACACTTACATTCCTATCAAAATTCTA[T/C]
GTTTATCCTATTCTTACGTTTTCTCAATCCTGCGATGAACGTGCAGAGATGTTGCCTAGAGGGGGGGGGGTGAATAGGCTTTCCTGAAATTTTCTCAACA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	28.40%	14.70%	0.28%	56.58%	NA
All Indica	2759	8.70%	2.50%	0.36%	88.40%	NA
All Japonica	1512	48.60%	40.40%	0.07%	10.91%	NA
Aus	269	88.80%	0.00%	0.00%	11.15%	NA
Indica I	595	0.50%	4.20%	0.84%	94.45%	NA
Indica II	465	4.50%	2.80%	0.00%	92.69%	NA
Indica III	913	15.70%	0.80%	0.11%	83.46%	NA
Indica Intermediate	786	9.40%	3.10%	0.51%	87.02%	NA
Temperate Japonica	767	45.80%	52.90%	0.00%	1.30%	NA
Tropical Japonica	504	58.50%	11.70%	0.00%	29.76%	NA
Japonica Intermediate	241	36.90%	60.60%	0.41%	2.07%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	36.70%	16.70%	2.22%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0719821103	A -> DEL	N	N	silent_mutation	Average:10.002; most accessible tissue: Callus, score: 23.27	N	N	N	N
vg0719821103	A -> G	LOC_Os07g33190.1	downstream_gene_variant ; 2080.0bp to feature; MODIFIER	silent_mutation	Average:10.002; most accessible tissue: Callus, score: 23.27	N	N	N	N
vg0719821103	A -> G	LOC_Os07g33190-LOC_Os07g33200	intergenic_region ; MODIFIER	silent_mutation	Average:10.002; most accessible tissue: Callus, score: 23.27	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0719821103	4.10E-06	NA	Spikelet_length	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
vg0719821103	9.51E-07	NA	Spikelet_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
vg0719821103	8.66E-06	8.66E-06	mr1362	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
vg0719821103	NA	4.07E-09	mr1709_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