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Detailed information for vg1224600619:

Variant ID: vg1224600619 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24600619
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: 82. )

Flanking Sequence (100 bp) in Reference Genome:

TATTTGCTCACAGTTCCGGCCCGTTTGATACCCGATAAAGCAAATCTTGGTTTCGGTTCCCTTGCGATGGGCCTGGGCGAGGGGGAACATGTTAAGTATC[C/T]
GCCTGGGATCATGTTTTCTTAGGTCTATTCTAGATGTACAATTTCATTTCGGTAGTCATTTTCCATTTTAGTTGGAAAATGCAGTTGGATGTTTAGGGTA

Reverse complement sequence

TACCCTAAACATCCAACTGCATTTTCCAACTAAAATGGAAAATGACTACCGAAATGAAATTGTACATCTAGAATAGACCTAAGAAAACATGATCCCAGGC[G/A]
GATACTTAACATGTTCCCCCTCGCCCAGGCCCATCGCAAGGGAACCGAAACCAAGATTTGCTTTATCGGGTATCAAACGGGCCGGAACTGTGAGCAAATA

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	86.00%	12.30%	0.95%	0.74%	NA
All Indica	2759	77.60%	20.80%	1.56%	0.04%	NA
All Japonica	1512	98.70%	0.10%	0.07%	1.19%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.00%	3.00%	1.01%	0.00%	NA
Indica II	465	73.50%	22.20%	4.30%	0.00%	NA
Indica III	913	60.40%	39.10%	0.55%	0.00%	NA
Indica Intermediate	786	86.30%	12.10%	1.53%	0.13%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	96.40%	0.20%	0.00%	3.37%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	84.40%	0.00%	0.00%	15.62%	NA
Intermediate	90	90.00%	7.80%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1224600619	C -> DEL	N	N	silent_mutation	Average:51.008; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg1224600619	C -> T	LOC_Os12g39810.1	upstream_gene_variant ; 4686.0bp to feature; MODIFIER	silent_mutation	Average:51.008; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg1224600619	C -> T	LOC_Os12g39800-LOC_Os12g39810	intergenic_region ; MODIFIER	silent_mutation	Average:51.008; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224600619	7.26E-07	NA	mr1623_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
vg1224600619	2.36E-07	4.47E-06	mr1623_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