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Detailed information for vg0805790429:

Variant ID: vg0805790429 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5790429
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

TTAGTGATTAATTACCTAATTAACTATTAACTAATAATAAATAGTGATTAATTATCTTGATTAGCGATTATTAATTAATCAATAATTAATAACTAATTAA[C/T]
CATTTTGAAATCCAGTATCGCTCTCTGGCTCAATGAGACCATTCGGTTTCGCTCTTCCGTTCCACGAGATAGCGCACGGTCTTGCACTTTCCCAGTGCGA

Reverse complement sequence

TCGCACTGGGAAAGTGCAAGACCGTGCGCTATCTCGTGGAACGGAAGAGCGAAACCGAATGGTCTCATTGAGCCAGAGAGCGATACTGGATTTCAAAATG[G/A]
TTAATTAGTTATTAATTATTGATTAATTAATAATCGCTAATCAAGATAATTAATCACTATTTATTATTAGTTAATAGTTAATTAGGTAATTAATCACTAA

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	67.10%	32.60%	0.25%	0.00%	NA
All Indica	2759	57.00%	42.80%	0.18%	0.00%	NA
All Japonica	1512	91.50%	8.10%	0.46%	0.00%	NA
Aus	269	30.90%	69.10%	0.00%	0.00%	NA
Indica I	595	47.10%	52.90%	0.00%	0.00%	NA
Indica II	465	87.10%	12.90%	0.00%	0.00%	NA
Indica III	913	47.50%	52.20%	0.22%	0.00%	NA
Indica Intermediate	786	57.60%	42.00%	0.38%	0.00%	NA
Temperate Japonica	767	98.40%	0.80%	0.78%	0.00%	NA
Tropical Japonica	504	84.70%	15.30%	0.00%	0.00%	NA
Japonica Intermediate	241	83.40%	16.20%	0.41%	0.00%	NA
VI/Aromatic	96	68.80%	31.20%	0.00%	0.00%	NA
Intermediate	90	74.40%	25.60%	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
vg0805790429	C -> T	LOC_Os08g10010.1	upstream_gene_variant ; 1289.0bp to feature; MODIFIER	silent_mutation	Average:58.994; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg0805790429	C -> T	LOC_Os08g10010-LOC_Os08g10020	intergenic_region ; MODIFIER	silent_mutation	Average:58.994; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805790429	NA	1.58E-06	mr1363	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
vg0805790429	1.49E-06	1.49E-06	mr1333_2	Jap_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
vg0805790429	NA	8.68E-06	mr1346_2	Jap_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
vg0805790429	NA	7.66E-06	mr1830_2	Jap_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