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Detailed information for vg0807801032:

Variant ID: vg0807801032 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 7801032
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.86, G: 0.14, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

CAAGGAACCATCCTATGACATTATCAAAGAAGAATCATAACATATTAAACAAATAGATGGTAATTAATCTAACAAGATTAATACTCTTCAGAAATAATTA[G/C]
AAAATAAAATAACTATAGCAGGCTAGCTTTGTAGGTGTTTGATATAGTGCAAGGAGTAGGTCATGACTTGCCTTGCAGAACAAGGGCTTTAATTTGCTAA

Reverse complement sequence

TTAGCAAATTAAAGCCCTTGTTCTGCAAGGCAAGTCATGACCTACTCCTTGCACTATATCAAACACCTACAAAGCTAGCCTGCTATAGTTATTTTATTTT[C/G]
TAATTATTTCTGAAGAGTATTAATCTTGTTAGATTAATTACCATCTATTTGTTTAATATGTTATGATTCTTCTTTGATAATGTCATAGGATGGTTCCTTG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.70%	24.70%	0.55%	9.06%	NA
All Indica	2759	78.60%	7.00%	0.69%	13.74%	NA
All Japonica	1512	36.90%	62.70%	0.13%	0.26%	NA
Aus	269	84.80%	0.70%	1.12%	13.38%	NA
Indica I	595	95.80%	0.30%	0.34%	3.53%	NA
Indica II	465	51.20%	17.80%	1.29%	29.68%	NA
Indica III	913	75.00%	7.70%	0.99%	16.32%	NA
Indica Intermediate	786	85.90%	4.80%	0.25%	9.03%	NA
Temperate Japonica	767	40.30%	59.30%	0.13%	0.26%	NA
Tropical Japonica	504	26.60%	73.40%	0.00%	0.00%	NA
Japonica Intermediate	241	47.70%	51.00%	0.41%	0.83%	NA
VI/Aromatic	96	93.80%	1.00%	0.00%	5.21%	NA
Intermediate	90	68.90%	24.40%	2.22%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0807801032	G -> C	LOC_Os08g13130.1	intron_variant ; MODIFIER	silent_mutation	Average:23.201; most accessible tissue: Callus, score: 59.855	N	N	N	N
vg0807801032	G -> DEL	N	N	silent_mutation	Average:23.201; most accessible tissue: Callus, score: 59.855	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0807801032	NA	6.65E-09	mr1986	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
vg0807801032	NA	2.52E-07	mr1574_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
vg0807801032	NA	2.88E-08	mr1765_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