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Detailed information for vg0909468501:

Variant ID: vg0909468501 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9468501
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.08, others allele: 0.00, population size: 154. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTATTCTTGATTGTGACCTCATTGAGTGCGCGATAATCGACGCACATCCTCTTCGTCTTATCCTTTTTCTCCACAAAAATGACCGGAGCACCCCAAGG[T/C]
GAAGTACTCGGTCGAATGTACCCTTTCTGCAGTTGCTCATTGACCTGCTTCTTGACCTCTGCTAGTTCGTTGGCCGCCATCCTGTACGGTCTCTTGTAAA

Reverse complement sequence

TTTACAAGAGACCGTACAGGATGGCGGCCAACGAACTAGCAGAGGTCAAGAAGCAGGTCAATGAGCAACTGCAGAAAGGGTACATTCGACCGAGTACTTC[A/G]
CCTTGGGGTGCTCCGGTCATTTTTGTGGAGAAAAAGGATAAGACGAAGAGGATGTGCGTCGATTATCGCGCACTCAATGAGGTCACAATCAAGAATAAAT

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	78.10%	2.90%	10.92%	8.06%	NA
All Indica	2759	82.10%	3.20%	10.91%	3.77%	NA
All Japonica	1512	80.60%	0.10%	1.46%	17.86%	NA
Aus	269	28.30%	14.90%	56.13%	0.74%	NA
Indica I	595	90.40%	0.00%	5.38%	4.20%	NA
Indica II	465	79.10%	5.20%	12.47%	3.23%	NA
Indica III	913	80.60%	4.20%	11.72%	3.50%	NA
Indica Intermediate	786	79.30%	3.40%	13.23%	4.07%	NA
Temperate Japonica	767	84.60%	0.00%	0.52%	14.86%	NA
Tropical Japonica	504	75.20%	0.20%	2.58%	22.02%	NA
Japonica Intermediate	241	78.80%	0.40%	2.07%	18.67%	NA
VI/Aromatic	96	57.30%	3.10%	36.46%	3.12%	NA
Intermediate	90	85.60%	4.40%	7.78%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909468501	T -> DEL	LOC_Os09g15470.1	N	frameshift_variant	Average:25.304; most accessible tissue: Zhenshan97 flag leaf, score: 51.466	N	N	N	N
vg0909468501	T -> C	LOC_Os09g15470.1	synonymous_variant ; p.Ser688Ser; LOW	synonymous_codon	Average:25.304; most accessible tissue: Zhenshan97 flag leaf, score: 51.466	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909468501	1.97E-06	NA	mr1151_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