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Detailed information for vg0211308829:

Variant ID: vg0211308829 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 11308829
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

CCTGAAATCTATATTTGCATATCTGAAGTTTGCATTAAAACATCTTTTCTACTCGTTAAAAATCTTAAGCAAGATGTTATTTTAGGAACACCGTTTTTAT[C/G]
ACTCATTCGTCCCTTCCTTGTCACAACCGAAGATATTCAATTTGAGATAATGGGCAAACAGGTGAGCCTAAGATTTTCGTCTAACACAGATGAGATTCTT

Reverse complement sequence

AAGAATCTCATCTGTGTTAGACGAAAATCTTAGGCTCACCTGTTTGCCCATTATCTCAAATTGAATATCTTCGGTTGTGACAAGGAAGGGACGAATGAGT[G/C]
ATAAAAACGGTGTTCCTAAAATAACATCTTGCTTAAGATTTTTAACGAGTAGAAAAGATGTTTTAATGCAAACTTCAGATATGCAAATATAGATTTCAGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.70%	40.60%	1.16%	0.51%	NA
All Indica	2759	90.80%	6.50%	1.88%	0.87%	NA
All Japonica	1512	1.60%	98.40%	0.00%	0.00%	NA
Aus	269	55.80%	43.50%	0.74%	0.00%	NA
Indica I	595	94.80%	1.00%	3.19%	1.01%	NA
Indica II	465	92.50%	4.10%	2.15%	1.29%	NA
Indica III	913	86.50%	12.40%	0.44%	0.66%	NA
Indica Intermediate	786	91.60%	5.20%	2.42%	0.76%	NA
Temperate Japonica	767	0.80%	99.20%	0.00%	0.00%	NA
Tropical Japonica	504	2.80%	97.20%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	7.30%	92.70%	0.00%	0.00%	NA
Intermediate	90	46.70%	52.20%	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
vg0211308829	C -> G	LOC_Os02g19350.1	stop_gained ; p.Ser775*; HIGH	stop_gained	Average:15.983; most accessible tissue: Minghui63 flower, score: 18.795	N	N	N	N
vg0211308829	C -> DEL	LOC_Os02g19350.1	N	frameshift_variant	Average:15.983; most accessible tissue: Minghui63 flower, score: 18.795	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0211308829	4.17E-06	NA	mr1460_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