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Detailed information for vg0311637474:

Variant ID: vg0311637474 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 11637474
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTATGTTTTTATCATTAAACTAGCACATAAGTAAAAGAGAGGGGTAATATTGTCAATTTCAAAAATATTTAACGGTCAACTAACGGAATGGGCATAGAG[G/A]
AGATCAAAATAAAAACTCATGGATATATAAAGGATGAGGCTAAATTCAGGGGTATATAAAGGATTGGACGAATTCTCAAGAGTACATAGGAATTTTTCTC

Reverse complement sequence

GAGAAAAATTCCTATGTACTCTTGAGAATTCGTCCAATCCTTTATATACCCCTGAATTTAGCCTCATCCTTTATATATCCATGAGTTTTTATTTTGATCT[C/T]
CTCTATGCCCATTCCGTTAGTTGACCGTTAAATATTTTTGAAATTGACAATATTACCCCTCTCTTTTACTTATGTGCTAGTTTAATGATAAAAACATAAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.30%	10.40%	1.35%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.04%	0.00%	NA
All Japonica	1512	65.20%	30.80%	3.97%	0.00%	NA
Aus	269	98.50%	1.50%	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	99.20%	0.60%	0.13%	0.00%	NA
Temperate Japonica	767	44.30%	48.80%	6.91%	0.00%	NA
Tropical Japonica	504	98.20%	1.40%	0.40%	0.00%	NA
Japonica Intermediate	241	62.70%	35.30%	2.07%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	86.70%	10.00%	3.33%	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
vg0311637474	G -> A	LOC_Os03g20530.1	upstream_gene_variant ; 1915.0bp to feature; MODIFIER	silent_mutation	Average:62.428; most accessible tissue: Minghui63 root, score: 88.035	N	N	N	N
vg0311637474	G -> A	LOC_Os03g20540.1	upstream_gene_variant ; 4226.0bp to feature; MODIFIER	silent_mutation	Average:62.428; most accessible tissue: Minghui63 root, score: 88.035	N	N	N	N
vg0311637474	G -> A	LOC_Os03g20530-LOC_Os03g20540	intergenic_region ; MODIFIER	silent_mutation	Average:62.428; most accessible tissue: Minghui63 root, score: 88.035	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0311637474	NA	7.64E-06	Yield	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
vg0311637474	NA	4.55E-07	mr1138	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
vg0311637474	NA	1.50E-06	mr1382	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
vg0311637474	NA	1.12E-06	mr1382	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
vg0311637474	6.42E-06	NA	mr1955	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
vg0311637474	NA	2.59E-08	mr1138_2	Jap_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
vg0311637474	2.20E-06	NA	mr1354_2	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
vg0311637474	NA	1.51E-07	mr1354_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
vg0311637474	NA	2.12E-21	mr1679_2	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
vg0311637474	NA	6.35E-07	mr1705_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