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Detailed information for vg0322579188:

Variant ID: vg0322579188 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 22579188
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

ATTGTAAATATCTCTGGATCAATACAACTACTCTTGGCGCATCGCTACCCTCTTTACCGAGGTTTTTACTTATCATCCGGCGGAATTTGGCACCTGACGC[G/A]
GGGCTGCATCGGTTCAGTTTGATCTCCAGCGAAGGGGTAAGTCCTATGTTCCGCTGGCCCTGGTGAATCTATCGGCTACGTTGGTGTTGTTTAAGGTTGC

Reverse complement sequence

GCAACCTTAAACAACACCAACGTAGCCGATAGATTCACCAGGGCCAGCGGAACATAGGACTTACCCCTTCGCTGGAGATCAAACTGAACCGATGCAGCCC[C/T]
GCGTCAGGTGCCAAATTCCGCCGGATGATAAGTAAAAACCTCGGTAAAGAGGGTAGCGATGCGCCAAGAGTAGTTGTATTGATCCAGAGATATTTACAAT

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	94.30%	4.90%	0.17%	0.57%	NA
All Indica	2759	98.00%	0.80%	0.29%	0.94%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	23.00%	76.60%	0.00%	0.37%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.60%	0.00%	0.00%	0.43%	NA
Indica III	913	97.20%	0.40%	0.44%	1.97%	NA
Indica Intermediate	786	96.70%	2.20%	0.38%	0.76%	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	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	0.00%	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
vg0322579188	G -> A	LOC_Os03g40610-LOC_Os03g40630	intergenic_region ; MODIFIER	silent_mutation	Average:39.522; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0322579188	G -> DEL	N	N	silent_mutation	Average:39.522; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0322579188	NA	1.64E-16	mr1158	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
vg0322579188	NA	1.25E-12	mr1499	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
vg0322579188	2.80E-06	NA	mr1248_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
vg0322579188	NA	7.47E-20	mr1305_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
vg0322579188	2.15E-06	NA	mr1406_2	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
vg0322579188	NA	8.09E-07	mr1603_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
vg0322579188	NA	5.60E-06	mr1608_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
vg0322579188	NA	1.31E-29	mr1757_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
vg0322579188	NA	1.17E-07	mr1762_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
vg0322579188	NA	6.29E-10	mr1818_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
vg0322579188	NA	1.46E-13	mr1846_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
vg0322579188	NA	4.64E-11	mr1897_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
vg0322579188	6.93E-06	2.29E-07	mr1921_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
vg0322579188	NA	3.48E-19	mr1927_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