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Detailed information for vg0800131056:

Variant ID: vg0800131056 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 131056
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: 127. )

Flanking Sequence (100 bp) in Reference Genome:

CATGACGTGGCGGGGCTCGGTGGCAAAGATGAAGCTGTTTTCTAGTCCTTGTCGAAGACATGGAACGTCTCCCTCTGCTCCCCTCCTCTTAGTCCTTGTC[C/T]
TTCATCTAATCATTTAGTGCGCTATTAGGTCCAGGAACTTGTAGAAGTTGATGATGCCACCTCGCTAATAATGTCTTGTAGCTCCGCCTTCGTCGGGATC

Reverse complement sequence

GATCCCGACGAAGGCGGAGCTACAAGACATTATTAGCGAGGTGGCATCATCAACTTCTACAAGTTCCTGGACCTAATAGCGCACTAAATGATTAGATGAA[G/A]
GACAAGGACTAAGAGGAGGGGAGCAGAGGGAGACGTTCCATGTCTTCGACAAGGACTAGAAAACAGCTTCATCTTTGCCACCGAGCCCCGCCACGTCATG

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	89.20%	10.70%	0.15%	0.00%	NA
All Indica	2759	82.40%	17.40%	0.18%	0.00%	NA
All Japonica	1512	99.10%	0.80%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	92.10%	7.90%	0.00%	0.00%	NA
Indica II	465	40.20%	58.90%	0.86%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	80.50%	19.30%	0.13%	0.00%	NA
Temperate Japonica	767	98.70%	1.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	12.20%	1.11%	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
vg0800131056	C -> T	LOC_Os08g01180-LOC_Os08g01190	intergenic_region ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0800131056	6.72E-06	NA	mr1138	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
vg0800131056	NA	7.11E-07	mr1728	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