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Detailed information for vg0325685596:

Variant ID: vg0325685596 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 25685596
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAACAATCAACCGTGACGGGCATACAAGTAATCTCTATCGGGCCTTAATAAAACGCCGTCAAAAAAGAGTGTCATCTGTGACGGGCAATAAACTTATCTC[C/A]
ATCGGGCCTCTAGTTGGAGCCCGTCACAGATGACCCTCATCTGTGACGGGCTTCTTTTAGGGCCCGATTGAGATATGGAACCCTCATCTCAATCGGGCCT

Reverse complement sequence

AGGCCCGATTGAGATGAGGGTTCCATATCTCAATCGGGCCCTAAAAGAAGCCCGTCACAGATGAGGGTCATCTGTGACGGGCTCCAACTAGAGGCCCGAT[G/T]
GAGATAAGTTTATTGCCCGTCACAGATGACACTCTTTTTTGACGGCGTTTTATTAAGGCCCGATAGAGATTACTTGTATGCCCGTCACGGTTGATTGTTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.20%	12.60%	1.16%	0.00%	NA
All Indica	2759	97.50%	2.50%	0.00%	0.00%	NA
All Japonica	1512	70.60%	28.90%	0.46%	0.00%	NA
Aus	269	75.50%	24.20%	0.37%	0.00%	NA
Indica I	595	98.70%	1.30%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	93.00%	7.00%	0.00%	0.00%	NA
Temperate Japonica	767	72.20%	27.60%	0.13%	0.00%	NA
Tropical Japonica	504	74.60%	24.60%	0.79%	0.00%	NA
Japonica Intermediate	241	57.30%	41.90%	0.83%	0.00%	NA
VI/Aromatic	96	37.50%	17.70%	44.79%	0.00%	NA
Intermediate	90	85.60%	10.00%	4.44%	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
vg0325685596	C -> A	LOC_Os03g45510.1	upstream_gene_variant ; 750.0bp to feature; MODIFIER	silent_mutation	Average:33.629; most accessible tissue: Minghui63 young leaf, score: 53.016	N	N	N	N
vg0325685596	C -> A	LOC_Os03g45519.1	downstream_gene_variant ; 565.0bp to feature; MODIFIER	silent_mutation	Average:33.629; most accessible tissue: Minghui63 young leaf, score: 53.016	N	N	N	N
vg0325685596	C -> A	LOC_Os03g45510-LOC_Os03g45519	intergenic_region ; MODIFIER	silent_mutation	Average:33.629; most accessible tissue: Minghui63 young leaf, score: 53.016	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0325685596	5.14E-06	2.67E-06	mr1765	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
vg0325685596	NA	8.70E-06	mr1223_2	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