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Detailed information for vg1119775301:

Variant ID: vg1119775301 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19775301
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.70, T: 0.30, others allele: 0.00, population size: 47. )

Flanking Sequence (100 bp) in Reference Genome:

TCGACTTAAGAGGACTGCACGAAAAAATCGATTTTCGCGTGCGGACTTTTTACGTGGACCGCACAAGAAACTACCTTCCTCCTTTCCCTCCCACCCACTT[T/C]
AAAATTTTCACATCGTCTCTCTTCCTTTTTCCTCCCTTTTATTCTCCCTCAACCACTCCCTTCTCTCTCTACCTTATCTCCCTCAACCACCGGCTTCCCA

Reverse complement sequence

TGGGAAGCCGGTGGTTGAGGGAGATAAGGTAGAGAGAGAAGGGAGTGGTTGAGGGAGAATAAAAGGGAGGAAAAAGGAAGAGAGACGATGTGAAAATTTT[A/G]
AAGTGGGTGGGAGGGAAAGGAGGAAGGTAGTTTCTTGTGCGGTCCACGTAAAAAGTCCGCACGCGAAAATCGATTTTTTCGTGCAGTCCTCTTAAGTCGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.50%	25.00%	0.38%	35.06%	NA
All Indica	2759	63.40%	5.50%	0.29%	30.74%	NA
All Japonica	1512	4.00%	53.40%	0.46%	42.13%	NA
Aus	269	6.30%	46.10%	0.00%	47.58%	NA
Indica I	595	84.90%	6.40%	0.17%	8.57%	NA
Indica II	465	58.30%	3.70%	0.22%	37.85%	NA
Indica III	913	58.10%	3.70%	0.11%	38.12%	NA
Indica Intermediate	786	56.50%	8.10%	0.64%	34.73%	NA
Temperate Japonica	767	4.70%	79.10%	0.65%	15.51%	NA
Tropical Japonica	504	3.40%	23.60%	0.40%	72.62%	NA
Japonica Intermediate	241	2.90%	34.00%	0.00%	63.07%	NA
VI/Aromatic	96	4.20%	68.80%	0.00%	27.08%	NA
Intermediate	90	41.10%	35.60%	3.33%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1119775301	T -> DEL	N	N	silent_mutation	Average:60.811; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg1119775301	T -> C	LOC_Os11g33410.1	upstream_gene_variant ; 2009.0bp to feature; MODIFIER	silent_mutation	Average:60.811; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N
vg1119775301	T -> C	LOC_Os11g33410-LOC_Os11g33420	intergenic_region ; MODIFIER	silent_mutation	Average:60.811; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119775301	NA	2.02E-07	mr1364	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