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Detailed information for vg0405796986:

Variant ID: vg0405796986 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5796986
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.81, A: 0.19, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

ATTAAGCTTATGCTGAATTTGGTGGTGGCACTGATCGGTGCTTGATGAGGACATTAGTGCCGGCTTTAGTCGTTGTTGGCACCAAGGTAACGTGTGTTGC[G/A]
GTCGTAGGGTGCTGGTGATGAAGAACACAGTACGGCGGCGGCGATGGGAATTGCCAAGATGGAGTTTGCCCTTCGATTCCCCTTAGCGCTCCTTAGGATC

Reverse complement sequence

GATCCTAAGGAGCGCTAAGGGGAATCGAAGGGCAAACTCCATCTTGGCAATTCCCATCGCCGCCGCCGTACTGTGTTCTTCATCACCAGCACCCTACGAC[C/T]
GCAACACACGTTACCTTGGTGCCAACAACGACTAAAGCCGGCACTAATGTCCTCATCAAGCACCGATCAGTGCCACCACCAAATTCAGCATAAGCTTAAT

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	52.20%	31.50%	0.61%	15.70%	NA
All Indica	2759	42.90%	47.70%	0.62%	8.84%	NA
All Japonica	1512	79.70%	0.50%	0.46%	19.31%	NA
Aus	269	10.00%	33.10%	0.74%	56.13%	NA
Indica I	595	12.40%	75.50%	1.18%	10.92%	NA
Indica II	465	42.80%	53.80%	0.00%	3.44%	NA
Indica III	913	64.40%	27.50%	0.11%	8.00%	NA
Indica Intermediate	786	41.00%	46.40%	1.15%	11.45%	NA
Temperate Japonica	767	90.50%	0.10%	0.13%	9.26%	NA
Tropical Japonica	504	60.50%	0.60%	0.99%	37.90%	NA
Japonica Intermediate	241	85.50%	1.70%	0.41%	12.45%	NA
VI/Aromatic	96	5.20%	47.90%	2.08%	44.79%	NA
Intermediate	90	53.30%	32.20%	1.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405796986	G -> DEL	N	N	silent_mutation	Average:41.645; most accessible tissue: Minghui63 young leaf, score: 73.49	N	N	N	N
vg0405796986	G -> A	LOC_Os04g10660-LOC_Os04g10680	intergenic_region ; MODIFIER	silent_mutation	Average:41.645; most accessible tissue: Minghui63 young leaf, score: 73.49	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405796986	NA	5.43E-06	mr1798	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
vg0405796986	3.68E-06	9.67E-08	mr1062_2	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
vg0405796986	NA	5.03E-06	mr1078_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
vg0405796986	NA	1.35E-06	mr1200_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
vg0405796986	NA	5.36E-07	mr1212_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
vg0405796986	NA	2.66E-06	mr1525_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