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Detailed information for vg1010328250:

Variant ID: vg1010328250 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 10328250
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, G: 0.08, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

TACTACAATTTCCACAGGATGTTACTGTCAAAACTGCAGTAACAACCTATATATTTATGCAGTAACAACCTATATATTTCCGCAGTAACATGACGAGTTA[G/C]
TGCACTTTTACAATAATGTTACTACTGGAACGTAATAACAGACTATAAGTGTCACGACAATATAAGTGATTTGCTCAAACGAAGTTTGAATCGATATATA

Reverse complement sequence

TATATATCGATTCAAACTTCGTTTGAGCAAATCACTTATATTGTCGTGACACTTATAGTCTGTTATTACGTTCCAGTAGTAACATTATTGTAAAAGTGCA[C/G]
TAACTCGTCATGTTACTGCGGAAATATATAGGTTGTTACTGCATAAATATATAGGTTGTTACTGCAGTTTTGACAGTAACATCCTGTGGAAATTGTAGTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.70%	4.50%	10.22%	19.57%	NA
All Indica	2759	55.20%	0.20%	16.42%	28.16%	NA
All Japonica	1512	86.10%	13.20%	0.40%	0.26%	NA
Aus	269	43.90%	0.00%	6.32%	49.81%	NA
Indica I	595	67.90%	0.00%	17.65%	14.45%	NA
Indica II	465	50.30%	0.40%	18.49%	30.75%	NA
Indica III	913	47.20%	0.40%	16.43%	35.93%	NA
Indica Intermediate	786	57.80%	0.00%	14.25%	27.99%	NA
Temperate Japonica	767	77.80%	21.80%	0.13%	0.26%	NA
Tropical Japonica	504	98.80%	0.40%	0.60%	0.20%	NA
Japonica Intermediate	241	85.90%	12.90%	0.83%	0.41%	NA
VI/Aromatic	96	92.70%	0.00%	2.08%	5.21%	NA
Intermediate	90	82.20%	6.70%	5.56%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1010328250	G -> C	LOC_Os10g20500.1	downstream_gene_variant ; 1686.0bp to feature; MODIFIER	silent_mutation	Average:71.817; most accessible tissue: Minghui63 flag leaf, score: 82.289	N	N	N	N
vg1010328250	G -> C	LOC_Os10g20480-LOC_Os10g20500	intergenic_region ; MODIFIER	silent_mutation	Average:71.817; most accessible tissue: Minghui63 flag leaf, score: 82.289	N	N	N	N
vg1010328250	G -> DEL	N	N	silent_mutation	Average:71.817; most accessible tissue: Minghui63 flag leaf, score: 82.289	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1010328250	1.79E-06	1.94E-06	mr1412	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