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Detailed information for vg0430779487:

Variant ID: vg0430779487 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 30779487
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 57. )

Flanking Sequence (100 bp) in Reference Genome:

ACTCTGTTTTTTCTTTTTCTCTGATTAATGTGAGAATTTCTAAGCCATGAAAGCGAACGTGAAGGCTCCTTTTTCTATTCCTTTAATTATATAATAGATA[G/A]
ATTAGCTGTAAGGTTAGCTACAATTTTTTTTTCCTCTCTCTATTTCTCACTTATACATTTAATGCATTTGTCTTGGAGATTATGTTAAACTAGCTCTTGC

Reverse complement sequence

GCAAGAGCTAGTTTAACATAATCTCCAAGACAAATGCATTAAATGTATAAGTGAGAAATAGAGAGAGGAAAAAAAAATTGTAGCTAACCTTACAGCTAAT[C/T]
TATCTATTATATAATTAAAGGAATAGAAAAAGGAGCCTTCACGTTCGCTTTCATGGCTTAGAAATTCTCACATTAATCAGAGAAAAAGAAAAAACAGAGT

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	31.90%	11.00%	21.79%	35.29%	NA
All Indica	2759	26.60%	11.60%	27.47%	34.25%	NA
All Japonica	1512	41.30%	10.40%	11.64%	36.64%	NA
Aus	269	4.10%	14.10%	30.11%	51.67%	NA
Indica I	595	2.50%	9.10%	38.32%	50.08%	NA
Indica II	465	74.00%	3.70%	7.31%	15.05%	NA
Indica III	913	18.90%	19.50%	29.90%	31.65%	NA
Indica Intermediate	786	25.80%	9.20%	28.37%	36.64%	NA
Temperate Japonica	767	63.00%	1.80%	9.65%	25.55%	NA
Tropical Japonica	504	15.10%	19.00%	15.87%	50.00%	NA
Japonica Intermediate	241	27.00%	19.90%	9.13%	43.98%	NA
VI/Aromatic	96	91.70%	1.00%	3.12%	4.17%	NA
Intermediate	90	53.30%	4.40%	13.33%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0430779487	G -> DEL	N	N	silent_mutation	Average:68.438; most accessible tissue: Callus, score: 87.682	N	N	N	N
vg0430779487	G -> A	LOC_Os04g51890.1	upstream_gene_variant ; 4149.0bp to feature; MODIFIER	silent_mutation	Average:68.438; most accessible tissue: Callus, score: 87.682	N	N	N	N
vg0430779487	G -> A	LOC_Os04g51880-LOC_Os04g51890	intergenic_region ; MODIFIER	silent_mutation	Average:68.438; most accessible tissue: Callus, score: 87.682	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0430779487	NA	9.58E-22	Grain_length	Ind_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
vg0430779487	NA	3.25E-06	mr1050	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
vg0430779487	NA	1.85E-06	mr1057	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
vg0430779487	NA	8.70E-09	mr1607	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
vg0430779487	NA	1.69E-08	mr1629	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
vg0430779487	NA	2.32E-06	mr1887	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
vg0430779487	NA	3.05E-08	mr1942	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
vg0430779487	NA	8.21E-06	mr1057_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
vg0430779487	NA	3.49E-07	mr1174_2	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
vg0430779487	NA	5.91E-07	mr1347_2	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
vg0430779487	NA	7.04E-06	mr1383_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
vg0430779487	6.17E-06	3.28E-08	mr1446_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
vg0430779487	NA	3.11E-12	mr1530_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
vg0430779487	NA	2.02E-07	mr1895_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
vg0430779487	NA	7.14E-06	mr1977_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