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Detailed information for vg0416659011:

Variant ID: vg0416659011 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 16659011
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: 336. )

Flanking Sequence (100 bp) in Reference Genome:

AACAACATAAGTCTAGACATACCCAATCTGGCACCATAAGGGCCGACATGAGGGATGAAGACTATACTAGCCGTTGACTATGTGTTGGAGATCCATGCCG[G/A]
CAAGTCGACGCCGACTAGATTAGGTCATCCCAGCTATTGTGCTCGTGTGATACTGATATATAAAGGCAACACCGACTGTGGAGATTATGGGTACCACATA

Reverse complement sequence

TATGTGGTACCCATAATCTCCACAGTCGGTGTTGCCTTTATATATCAGTATCACACGAGCACAATAGCTGGGATGACCTAATCTAGTCGGCGTCGACTTG[C/T]
CGGCATGGATCTCCAACACATAGTCAACGGCTAGTATAGTCTTCATCCCTCATGTCGGCCCTTATGGTGCCAGATTGGGTATGTCTAGACTTATGTTGTT

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	97.70%	1.60%	0.63%	0.00%	NA
All Indica	2759	99.30%	0.40%	0.29%	0.00%	NA
All Japonica	1512	94.20%	4.40%	1.39%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.50%	0.80%	0.67%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.60%	0.25%	0.00%	NA
Temperate Japonica	767	91.00%	6.90%	2.09%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	93.80%	4.10%	2.07%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	1.11%	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
vg0416659011	G -> A	LOC_Os04g28190-LOC_Os04g28210	intergenic_region ; MODIFIER	silent_mutation	Average:64.771; most accessible tissue: Zhenshan97 young leaf, score: 87.859	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0416659011	2.73E-06	NA	mr1549	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
vg0416659011	NA	4.21E-06	mr1550	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
vg0416659011	7.95E-07	1.36E-10	mr1757	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
vg0416659011	NA	1.09E-06	mr1549_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