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Detailed information for vg1110436569:

Variant ID: vg1110436569 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10436569
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

GCTCTGACTGTATGGAACATACACACAGTAGGTGGCTAAAGAAATCAAGAAAGATGGTTTAAATGGGTCATAGGAGATGGCTCCCCCTACGGCACGCCTT[T/C]
AGAAGAAAGAAGAAAATTTTCAATGGTAAGAAAGAACTTGGGTCTGCCCCTGCGGATTTGTCCGGAGATCAGGTACACAATATGGTGAAGGACATTACTA

Reverse complement sequence

TAGTAATGTCCTTCACCATATTGTGTACCTGATCTCCGGACAAATCCGCAGGGGCAGACCCAAGTTCTTTCTTACCATTGAAAATTTTCTTCTTTCTTCT[A/G]
AAGGCGTGCCGTAGGGGGAGCCATCTCCTATGACCCATTTAAACCATCTTTCTTGATTTCTTTAGCCACCTACTGTGTGTATGTTCCATACAGTCAGAGC

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	93.10%	5.50%	1.31%	0.00%	NA
All Indica	2759	89.40%	8.40%	2.25%	0.00%	NA
All Japonica	1512	98.40%	1.60%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	88.40%	10.10%	1.51%	0.00%	NA
Indica II	465	95.90%	4.10%	0.00%	0.00%	NA
Indica III	913	83.00%	11.70%	5.26%	0.00%	NA
Indica Intermediate	786	93.60%	5.70%	0.64%	0.00%	NA
Temperate Japonica	767	98.60%	1.40%	0.00%	0.00%	NA
Tropical Japonica	504	97.40%	2.60%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg1110436569	T -> C	LOC_Os11g18510.1	synonymous_variant ; p.Phe366Phe; LOW	synonymous_codon	Average:29.764; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110436569	9.81E-07	9.81E-07	mr1417	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
vg1110436569	NA	8.54E-06	mr1677	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
vg1110436569	NA	1.62E-06	mr1361_2	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