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Detailed information for vg0313852227:

Variant ID: vg0313852227 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 13852227
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCACAAGACTTAGGGGGAGAATGATGGATAAGTCTTTGTGGTCCTTGGTCGTGGTTCTTCCTTTTCTTTTGAGTAGTTTCACCTTTTCAGGACAGCATCT[A/G]
CTTCTTTAGCATATTTTCAGTTGCTAGGACAGCTGCGGTTAGTAGGACAGCAGCAGTTAGCATCTTCTTTATACCTCCTTTATGCTTTATTCAATTTGGA

Reverse complement sequence

TCCAAATTGAATAAAGCATAAAGGAGGTATAAAGAAGATGCTAACTGCTGCTGTCCTACTAACCGCAGCTGTCCTAGCAACTGAAAATATGCTAAAGAAG[T/C]
AGATGCTGTCCTGAAAAGGTGAAACTACTCAAAAGAAAAGGAAGAACCACGACCAAGGACCACAAAGACTTATCCATCATTCTCCCCCTAAGTCTTGTGC

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	70.20%	29.70%	0.06%	0.00%	NA
All Indica	2759	99.60%	0.40%	0.00%	0.00%	NA
All Japonica	1512	16.00%	83.90%	0.07%	0.00%	NA
Aus	269	98.50%	1.10%	0.37%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.50%	0.00%	0.00%	NA
Temperate Japonica	767	25.90%	73.90%	0.13%	0.00%	NA
Tropical Japonica	504	4.00%	96.00%	0.00%	0.00%	NA
Japonica Intermediate	241	9.50%	90.50%	0.00%	0.00%	NA
VI/Aromatic	96	13.50%	86.50%	0.00%	0.00%	NA
Intermediate	90	56.70%	42.20%	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
vg0313852227	A -> G	LOC_Os03g24339.1	intron_variant ; MODIFIER	silent_mutation	Average:46.178; most accessible tissue: Zhenshan97 flower, score: 68.734	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0313852227	NA	6.42E-11	mr1281	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
vg0313852227	3.80E-06	NA	mr1530	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
vg0313852227	NA	2.69E-07	mr1821_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