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Detailed information for vg1014030357:

Variant ID: vg1014030357 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 14030357
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: 227. )

Flanking Sequence (100 bp) in Reference Genome:

ATTCTATCTCAGGAATCTGGTCGCCTAAAAGAAAGTCCAGTGAAAAACAATGTTTTCAGTGTAAAATCAAATGTGTTTTTGATTATTATTCTGTGATGAA[C/T]
AATTGGGCATTGGAGATTATTGGTTTTGTTATTTGGAATTTATTCACGAAGTGGTTTTGGAGATGATTGGATTCACAGGTGATCACAGGGTTCATTATTT

Reverse complement sequence

AAATAATGAACCCTGTGATCACCTGTGAATCCAATCATCTCCAAAACCACTTCGTGAATAAATTCCAAATAACAAAACCAATAATCTCCAATGCCCAATT[G/A]
TTCATCACAGAATAATAATCAAAAACACATTTGATTTTACACTGAAAACATTGTTTTTCACTGGACTTTCTTTTAGGCGACCAGATTCCTGAGATAGAAT

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	46.40%	0.50%	25.18%	27.95%	NA
All Indica	2759	16.60%	0.10%	40.67%	42.59%	NA
All Japonica	1512	97.10%	1.20%	1.32%	0.40%	NA
Aus	269	42.40%	0.00%	11.15%	46.47%	NA
Indica I	595	17.60%	0.20%	17.98%	64.20%	NA
Indica II	465	13.30%	0.00%	44.09%	42.58%	NA
Indica III	913	18.00%	0.20%	54.11%	27.71%	NA
Indica Intermediate	786	16.20%	0.10%	40.20%	43.51%	NA
Temperate Japonica	767	95.60%	2.30%	1.96%	0.13%	NA
Tropical Japonica	504	99.00%	0.00%	0.40%	0.60%	NA
Japonica Intermediate	241	97.90%	0.00%	1.24%	0.83%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	64.40%	0.00%	18.89%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1014030357	C -> T	LOC_Os10g26780-LOC_Os10g26800	intergenic_region ; MODIFIER	silent_mutation	Average:15.794; most accessible tissue: Callus, score: 29.855	N	N	N	N
vg1014030357	C -> DEL	N	N	silent_mutation	Average:15.794; most accessible tissue: Callus, score: 29.855	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1014030357	1.87E-06	6.04E-06	mr1528	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