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Detailed information for vg0817111129:

Variant ID: vg0817111129 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17111129
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.64, G: 0.37, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

GATGTGGAGATAATCATTTGACATTGCTTACATATTGAGTTCTAAAAATACAATATAATTATAAATAATATATCAGGTTTGCATGATATTTGTCGAGGAG[T/G]
GATCCTCTCTAGCGGGATATCGTGAGATCCCCCTTTTGTGAGTTCGGCTGGGGGAAAGATCTCGCCTCTAGAGTTCGCGTGTCCGCCCTGAAGGCTGCTA

Reverse complement sequence

TAGCAGCCTTCAGGGCGGACACGCGAACTCTAGAGGCGAGATCTTTCCCCCAGCCGAACTCACAAAAGGGGGATCTCACGATATCCCGCTAGAGAGGATC[A/C]
CTCCTCGACAAATATCATGCAAACCTGATATATTATTTATAATTATATTGTATTTTTAGAACTCAATATGTAAGCAATGTCAAATGATTATCTCCACATC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.20%	45.70%	0.02%	3.03%	NA
All Indica	2759	47.70%	50.00%	0.04%	2.28%	NA
All Japonica	1512	56.10%	42.90%	0.00%	1.06%	NA
Aus	269	77.70%	1.90%	0.00%	20.45%	NA
Indica I	595	74.80%	24.00%	0.00%	1.18%	NA
Indica II	465	12.90%	86.00%	0.00%	1.08%	NA
Indica III	913	50.70%	48.10%	0.00%	1.20%	NA
Indica Intermediate	786	44.30%	50.50%	0.13%	5.09%	NA
Temperate Japonica	767	68.70%	31.00%	0.00%	0.26%	NA
Tropical Japonica	504	44.80%	53.60%	0.00%	1.59%	NA
Japonica Intermediate	241	39.40%	58.10%	0.00%	2.49%	NA
VI/Aromatic	96	7.30%	87.50%	0.00%	5.21%	NA
Intermediate	90	46.70%	48.90%	0.00%	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
vg0817111129	T -> G	LOC_Os08g28060.1	upstream_gene_variant ; 3831.0bp to feature; MODIFIER	silent_mutation	Average:39.448; most accessible tissue: Zhenshan97 young leaf, score: 58.398	N	N	N	N
vg0817111129	T -> G	LOC_Os08g28070.1	intron_variant ; MODIFIER	silent_mutation	Average:39.448; most accessible tissue: Zhenshan97 young leaf, score: 58.398	N	N	N	N
vg0817111129	T -> DEL	N	N	silent_mutation	Average:39.448; most accessible tissue: Zhenshan97 young leaf, score: 58.398	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817111129	NA	1.76E-14	Grain_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
vg0817111129	3.61E-06	NA	mr1006	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
vg0817111129	7.29E-06	NA	mr1006	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
vg0817111129	4.53E-06	NA	mr1052	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
vg0817111129	7.62E-06	NA	mr1052	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
vg0817111129	NA	9.60E-06	mr1336	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