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Detailed information for vg0322105332:

Variant ID: vg0322105332 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 22105332
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

TGAAGATTCTTTGGGGCAACGATTAGTATTTAAAGTAGAGCGATAACGGACGGGAAAACAGCAAGTGCGGGTTTCTCTCAGAGTCGGTATATGGCAAATC[C/T]
GAAACATTATCCAATATTCCGGACTTAGGGGCATGTGTTAACGACCAAATTTGGTAAATTCTATCACTATTGGCATCGGAGGTGAGGATCAGATCGAAGT

Reverse complement sequence

ACTTCGATCTGATCCTCACCTCCGATGCCAATAGTGATAGAATTTACCAAATTTGGTCGTTAACACATGCCCCTAAGTCCGGAATATTGGATAATGTTTC[G/A]
GATTTGCCATATACCGACTCTGAGAGAAACCCGCACTTGCTGTTTTCCCGTCCGTTATCGCTCTACTTTAAATACTAATCGTTGCCCCAAAGAATCTTCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.10%	16.10%	26.83%	0.95%	NA
All Indica	2759	31.00%	27.30%	40.20%	1.56%	NA
All Japonica	1512	99.30%	0.10%	0.53%	0.13%	NA
Aus	269	84.40%	0.00%	15.61%	0.00%	NA
Indica I	595	12.30%	58.50%	28.91%	0.34%	NA
Indica II	465	22.80%	32.90%	43.01%	1.29%	NA
Indica III	913	42.50%	8.20%	46.55%	2.74%	NA
Indica Intermediate	786	36.50%	22.50%	39.69%	1.27%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	98.80%	0.20%	0.79%	0.20%	NA
Japonica Intermediate	241	98.30%	0.00%	1.24%	0.41%	NA
VI/Aromatic	96	11.50%	0.00%	88.54%	0.00%	NA
Intermediate	90	64.40%	8.90%	26.67%	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
vg0322105332	C -> T	LOC_Os03g39730.1	upstream_gene_variant ; 222.0bp to feature; MODIFIER	silent_mutation	Average:12.387; most accessible tissue: Zhenshan97 young leaf, score: 17.571	N	N	N	N
vg0322105332	C -> T	LOC_Os03g39720.1	downstream_gene_variant ; 4380.0bp to feature; MODIFIER	silent_mutation	Average:12.387; most accessible tissue: Zhenshan97 young leaf, score: 17.571	N	N	N	N
vg0322105332	C -> T	LOC_Os03g39730-LOC_Os03g39740	intergenic_region ; MODIFIER	silent_mutation	Average:12.387; most accessible tissue: Zhenshan97 young leaf, score: 17.571	N	N	N	N
vg0322105332	C -> DEL	N	N	silent_mutation	Average:12.387; most accessible tissue: Zhenshan97 young leaf, score: 17.571	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0322105332	3.81E-07	NA	mr1804	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
vg0322105332	5.82E-07	1.50E-07	mr1804	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