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Detailed information for vg1112750303:

Variant ID: vg1112750303 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 12750303
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

AATCCCAAGCTCCGCCAAAGTCAAGTGCACAAGCTCTCAACATATCTTCCAAGATTTGATTTACCCGCTCGGTCTGACTATCTGTTTGCGGATGATAAGC[T/C]
GTGCTGAAATTCAAACGAGTCCCCAATTCTTCTTGCAGTTTCTGCCAGAACTTTGAAGTGAATTGACTTCCTCGATCAGATACAATCTTCTTAGGTACCC

Reverse complement sequence

GGGTACCTAAGAAGATTGTATCTGATCGAGGAAGTCAATTCACTTCAAAGTTCTGGCAGAAACTGCAAGAAGAATTGGGGACTCGTTTGAATTTCAGCAC[A/G]
GCTTATCATCCGCAAACAGATAGTCAGACCGAGCGGGTAAATCAAATCTTGGAAGATATGTTGAGAGCTTGTGCACTTGACTTTGGCGGAGCTTGGGATT

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	36.40%	0.20%	33.73%	29.67%	NA
All Indica	2759	6.40%	0.00%	46.94%	46.65%	NA
All Japonica	1512	93.50%	0.20%	0.66%	5.62%	NA
Aus	269	3.00%	1.50%	91.82%	3.72%	NA
Indica I	595	9.60%	0.00%	26.39%	64.03%	NA
Indica II	465	6.50%	0.00%	61.29%	32.26%	NA
Indica III	913	3.50%	0.00%	51.04%	45.45%	NA
Indica Intermediate	786	7.40%	0.00%	49.24%	43.38%	NA
Temperate Japonica	767	96.20%	0.40%	0.65%	2.74%	NA
Tropical Japonica	504	87.70%	0.00%	0.79%	11.51%	NA
Japonica Intermediate	241	97.10%	0.00%	0.41%	2.49%	NA
VI/Aromatic	96	85.40%	1.00%	12.50%	1.04%	NA
Intermediate	90	45.60%	0.00%	33.33%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112750303	T -> DEL	LOC_Os11g22220.1	N	frameshift_variant	Average:11.414; most accessible tissue: Callus, score: 36.841	N	N	N	N
vg1112750303	T -> C	LOC_Os11g22220.1	synonymous_variant ; p.Thr910Thr; LOW	synonymous_codon	Average:11.414; most accessible tissue: Callus, score: 36.841	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112750303	4.16E-06	6.58E-06	mr1629_2	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