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Detailed information for vg1119255268:

Variant ID: vg1119255268 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19255268
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCACGAGGTCCTCGGAGCCAAACGAGGGCGCACGAACGCGGTGAAAACATGGGCCCCACCCCCCTCTCTCCTCACGCACGCAATCTGCTTACGTGGATAG[A/G]
CATTGCCACACGTGAGTCACGTGTGTGCACCGTGAATGCCCTAAGAGGTACTCCCCCGTTCCATTTTAAGTGCAGTTATGGGTTTGTGTCCAACGTTTGA

Reverse complement sequence

TCAAACGTTGGACACAAACCCATAACTGCACTTAAAATGGAACGGGGGAGTACCTCTTAGGGCATTCACGGTGCACACACGTGACTCACGTGTGGCAATG[T/C]
CTATCCACGTAAGCAGATTGCGTGCGTGAGGAGAGAGGGGGGTGGGGCCCATGTTTTCACCGCGTTCGTGCGCCCTCGTTTGGCTCCGAGGACCTCGTGA

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	98.10%	1.50%	0.49%	0.00%	NA
All Indica	2759	96.70%	2.50%	0.80%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.70%	0.00%	0.34%	0.00%	NA
Indica II	465	89.00%	8.20%	2.80%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	96.30%	2.80%	0.89%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	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
vg1119255268	A -> G	LOC_Os11g32630-LOC_Os11g32640	intergenic_region ; MODIFIER	silent_mutation	Average:70.34; most accessible tissue: Zhenshan97 panicle, score: 81.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119255268	NA	1.50E-06	mr1121	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
vg1119255268	NA	6.10E-06	mr1297	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
vg1119255268	NA	2.94E-06	mr1372	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
vg1119255268	NA	4.50E-06	mr1432	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
vg1119255268	4.41E-08	4.41E-08	mr1465	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
vg1119255268	NA	8.24E-06	mr1537	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
vg1119255268	NA	3.00E-06	mr1928	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
vg1119255268	NA	6.62E-06	mr1943	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
vg1119255268	NA	2.68E-07	mr1951	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
vg1119255268	NA	2.27E-07	mr1958	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