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Detailed information for vg1203926835:

Variant ID: vg1203926835 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 3926835
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTTCTGAGTTGTGTATGTCCAGATTCAAACCCAGAAGTGGGTTTTTTTAGGGAGTACGTGCTACTAACACCATGAACTCACGTTTCAACATATAATTTC[G/A]
TTTGGCTATTTAGGCTTAAGTGATTTATGTGATCAAGATGACGTGGGTGATGCAATAACTAGCAATATGAGCAAACATCATGATTTTTTATGCCCAAACT

Reverse complement sequence

AGTTTGGGCATAAAAAATCATGATGTTTGCTCATATTGCTAGTTATTGCATCACCCACGTCATCTTGATCACATAAATCACTTAAGCCTAAATAGCCAAA[C/T]
GAAATTATATGTTGAAACGTGAGTTCATGGTGTTAGTAGCACGTACTCCCTAAAAAAACCCACTTCTGGGTTTGAATCTGGACATACACAACTCAGAAGT

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	95.30%	4.30%	0.38%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.04%	0.00%	NA
All Japonica	1512	86.40%	12.60%	1.06%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	96.60%	2.60%	0.78%	0.00%	NA
Tropical Japonica	504	70.20%	29.20%	0.60%	0.00%	NA
Japonica Intermediate	241	87.60%	9.50%	2.90%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	7.80%	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
vg1203926835	G -> A	LOC_Os12g07770-LOC_Os12g07780	intergenic_region ; MODIFIER	silent_mutation	Average:36.235; most accessible tissue: Zhenshan97 flower, score: 58.632	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1203926835	NA	3.97E-08	mr1013	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
vg1203926835	NA	1.29E-06	mr1031	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
vg1203926835	NA	1.16E-07	mr1034	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
vg1203926835	NA	3.69E-07	mr1056	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