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Detailed information for vg0124002704:

Variant ID: vg0124002704 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 24002704
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.09, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

CTCCCAGTATCGCTTTTGAGAGCATTGAGTTGATAGTTGAGTTAGGGTTTCGAGTTTAGTTGAGATTTTCATAAGGAGTGTGGTTGTTGCACTTTGTAAA[C/T]
ACAGAGAGAAGTAATAAAGTTGTCATCTACTTTGAGAGATCTTCGATTTGTGTTTGCTCAGGTTCGGCGGTCTAACCGACGAAACACCGGTGGTCAGACC

Reverse complement sequence

GGTCTGACCACCGGTGTTTCGTCGGTTAGACCGCCGAACCTGAGCAAACACAAATCGAAGATCTCTCAAAGTAGATGACAACTTTATTACTTCTCTCTGT[G/A]
TTTACAAAGTGCAACAACCACACTCCTTATGAAAATCTCAACTAAACTCGAAACCCTAACTCAACTATCAACTCAATGCTCTCAAAAGCGATACTGGGAG

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	82.30%	17.60%	0.04%	0.00%	NA
All Indica	2759	72.60%	27.30%	0.07%	0.00%	NA
All Japonica	1512	98.40%	1.60%	0.00%	0.00%	NA
Aus	269	95.20%	4.80%	0.00%	0.00%	NA
Indica I	595	40.50%	59.50%	0.00%	0.00%	NA
Indica II	465	88.20%	11.60%	0.22%	0.00%	NA
Indica III	913	79.50%	20.50%	0.00%	0.00%	NA
Indica Intermediate	786	79.80%	20.10%	0.13%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	93.40%	6.60%	0.00%	0.00%	NA
VI/Aromatic	96	66.70%	33.30%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	0.00%	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
vg0124002704	C -> T	LOC_Os01g42310.1	intron_variant ; MODIFIER	silent_mutation	Average:57.848; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0124002704	NA	1.79E-06	mr1045_2	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
vg0124002704	NA	1.07E-06	mr1528_2	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
vg0124002704	NA	2.76E-06	mr1528_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
vg0124002704	NA	1.68E-06	mr1545_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
vg0124002704	NA	1.51E-08	mr1758_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