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Detailed information for vg0920856743:

Variant ID: vg0920856743 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 20856743
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.56, G: 0.44, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

ATCTGTGTGCCAAGATGAAATATGACTATCGAAAGTAGGTGGAGAAAGTACTACACCCTCTGTCCCATAATATAAGGGATTTTAAGTTTTTACTTATAAT[A/G]
TTTGACCACTTGTCTTATTCAAAAAATTTGTGCAAATATAAAAAACGAAAAGTTGTGCTTAAAGTATTTTGGATAATAAAGTAAGTCACAAAGAAAATAA

Reverse complement sequence

TTATTTTCTTTGTGACTTACTTTATTATCCAAAATACTTTAAGCACAACTTTTCGTTTTTTATATTTGCACAAATTTTTTGAATAAGACAAGTGGTCAAA[T/C]
ATTATAAGTAAAAACTTAAAATCCCTTATATTATGGGACAGAGGGTGTAGTACTTTCTCCACCTACTTTCGATAGTCATATTTCATCTTGGCACACAGAT

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	63.60%	36.20%	0.21%	0.00%	NA
All Indica	2759	44.40%	55.30%	0.29%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	39.40%	60.60%	0.00%	0.00%	NA
Indica I	595	11.80%	87.70%	0.50%	0.00%	NA
Indica II	465	59.80%	39.80%	0.43%	0.00%	NA
Indica III	913	57.60%	42.40%	0.00%	0.00%	NA
Indica Intermediate	786	44.70%	55.00%	0.38%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	81.10%	17.80%	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
vg0920856743	A -> G	LOC_Os09g36180.1	intron_variant ; MODIFIER	silent_mutation	Average:48.227; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0920856743	NA	5.83E-06	mr1398	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
vg0920856743	NA	5.11E-10	mr1050_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
vg0920856743	NA	2.23E-13	mr1904_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