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Detailed information for vg1001790923:

Variant ID: vg1001790923 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1790923
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

CTAATAGACCCATCGCCCAATCAACGGCTCAGATCGTGTTTCAGTCGATAAAAACAGTACTACCTCCGTTTCATAATGTAAGTCATTCTAGCATTGCCCA[C/T]
ATTCATATAGATACTAATGAATCTAAACATATATGTGTGTCTAGATTTATTAACATCTATATGAATGTGGATAATACTAGAAAGTCTTACATTATGAAAC

Reverse complement sequence

GTTTCATAATGTAAGACTTTCTAGTATTATCCACATTCATATAGATGTTAATAAATCTAGACACACATATATGTTTAGATTCATTAGTATCTATATGAAT[G/A]
TGGGCAATGCTAGAATGACTTACATTATGAAACGGAGGTAGTACTGTTTTTATCGACTGAAACACGATCTGAGCCGTTGATTGGGCGATGGGTCTATTAG

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	51.60%	17.80%	0.42%	30.13%	NA
All Indica	2759	29.80%	19.30%	0.69%	50.24%	NA
All Japonica	1512	94.40%	4.00%	0.07%	1.52%	NA
Aus	269	12.60%	87.00%	0.00%	0.37%	NA
Indica I	595	46.70%	3.00%	0.34%	49.92%	NA
Indica II	465	23.40%	14.40%	1.72%	60.43%	NA
Indica III	913	22.10%	32.20%	0.33%	45.35%	NA
Indica Intermediate	786	29.50%	19.60%	0.76%	50.13%	NA
Temperate Japonica	767	99.20%	0.10%	0.13%	0.52%	NA
Tropical Japonica	504	85.10%	11.50%	0.00%	3.37%	NA
Japonica Intermediate	241	98.80%	0.40%	0.00%	0.83%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	71.10%	13.30%	0.00%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001790923	C -> T	LOC_Os10g03930.1	upstream_gene_variant ; 2844.0bp to feature; MODIFIER	silent_mutation	Average:47.825; most accessible tissue: Zhenshan97 root, score: 81.974	N	N	N	N
vg1001790923	C -> T	LOC_Os10g03950.1	upstream_gene_variant ; 1292.0bp to feature; MODIFIER	silent_mutation	Average:47.825; most accessible tissue: Zhenshan97 root, score: 81.974	N	N	N	N
vg1001790923	C -> T	LOC_Os10g03930-LOC_Os10g03950	intergenic_region ; MODIFIER	silent_mutation	Average:47.825; most accessible tissue: Zhenshan97 root, score: 81.974	N	N	N	N
vg1001790923	C -> DEL	N	N	silent_mutation	Average:47.825; most accessible tissue: Zhenshan97 root, score: 81.974	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001790923	2.70E-07	NA	mr1486	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
vg1001790923	4.48E-07	NA	mr1548	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
vg1001790923	3.63E-09	NA	mr1486_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
vg1001790923	5.52E-10	1.85E-06	mr1588_2	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