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Detailed information for vg0803044175:

Variant ID: vg0803044175 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 3044175
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

TGGCTAATCATGGACTAATTAGACTCAAAAGATTCGTCTCGCAATTTTCCCCCTAACTGTGGAATTAGTTTTTTAATTTATCTATATTTAATACTATATG[T/C]
ATGTGTCCAAAGATTCAATGTGATGTTTTTGGGAAAAAGTTTTTGGAACTAAACAGGGCCTAATTTGCATAAAACTAGGATCGCAAACATTAATAGAGCT

Reverse complement sequence

AGCTCTATTAATGTTTGCGATCCTAGTTTTATGCAAATTAGGCCCTGTTTAGTTCCAAAAACTTTTTCCCAAAAACATCACATTGAATCTTTGGACACAT[A/G]
CATATAGTATTAAATATAGATAAATTAAAAAACTAATTCCACAGTTAGGGGGAAAATTGCGAGACGAATCTTTTGAGTCTAATTAGTCCATGATTAGCCA

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	66.80%	31.90%	1.33%	0.00%	NA
All Indica	2759	54.50%	43.80%	1.70%	0.00%	NA
All Japonica	1512	82.50%	16.80%	0.66%	0.00%	NA
Aus	269	97.80%	0.70%	1.49%	0.00%	NA
Indica I	595	55.00%	44.50%	0.50%	0.00%	NA
Indica II	465	68.80%	27.30%	3.87%	0.00%	NA
Indica III	913	50.90%	48.10%	0.99%	0.00%	NA
Indica Intermediate	786	49.70%	48.10%	2.16%	0.00%	NA
Temperate Japonica	767	78.60%	20.50%	0.91%	0.00%	NA
Tropical Japonica	504	86.10%	13.70%	0.20%	0.00%	NA
Japonica Intermediate	241	87.60%	11.60%	0.83%	0.00%	NA
VI/Aromatic	96	94.80%	4.20%	1.04%	0.00%	NA
Intermediate	90	55.60%	43.30%	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
vg0803044175	T -> C	LOC_Os08g05680.1	upstream_gene_variant ; 2334.0bp to feature; MODIFIER	silent_mutation	Average:55.497; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N
vg0803044175	T -> C	LOC_Os08g05670-LOC_Os08g05680	intergenic_region ; MODIFIER	silent_mutation	Average:55.497; most accessible tissue: Minghui63 panicle, score: 85.556	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0803044175	4.71E-06	4.71E-06	mr1027	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
vg0803044175	4.75E-06	NA	mr1510_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