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Detailed information for vg0309808587:

Variant ID: vg0309808587 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 9808587
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTTGATGACTTTGCTCTCCGTCTCAACACTCTCTTGCAGAAAATGGTGCAGTACGGCGACGACACCTACGACGAGGAGAGAGCTGTCGAGAAGCTCTT[T/C]
CGCTGCGTCCCAGAGAAGTACAGGCAGATCGCTCGCTCGATCGAATCTCTGCTGGACCTCTCCACGATGTCGATCGAGGAGGCGTTAGGTCGCCTCAAGG

Reverse complement sequence

CCTTGAGGCGACCTAACGCCTCCTCGATCGACATCGTGGAGAGGTCCAGCAGAGATTCGATCGAGCGAGCGATCTGCCTGTACTTCTCTGGGACGCAGCG[A/G]
AAGAGCTTCTCGACAGCTCTCTCCTCGTCGTAGGTGTCGTCGCCGTACTGCACCATTTTCTGCAAGAGAGTGTTGAGACGGAGAGCAAAGTCATCAACAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.40%	0.60%	0.93%	0.08%	NA
All Indica	2759	98.80%	0.70%	0.36%	0.14%	NA
All Japonica	1512	99.80%	0.10%	0.13%	0.00%	NA
Aus	269	87.00%	1.50%	11.52%	0.00%	NA
Indica I	595	99.30%	0.20%	0.34%	0.17%	NA
Indica II	465	98.90%	0.20%	0.43%	0.43%	NA
Indica III	913	98.70%	1.00%	0.33%	0.00%	NA
Indica Intermediate	786	98.50%	1.00%	0.38%	0.13%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	2.10%	1.04%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0309808587	T -> C	LOC_Os03g17634.1	intron_variant ; MODIFIER	silent_mutation	Average:30.779; most accessible tissue: Minghui63 root, score: 51.763	N	N	N	N
vg0309808587	T -> DEL	N	N	silent_mutation	Average:30.779; most accessible tissue: Minghui63 root, score: 51.763	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0309808587	3.20E-06	3.20E-06	mr1260	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