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Detailed information for vg1102756844:

Variant ID: vg1102756844 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 2756844
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTTAGCTCATAAAAAATTCTGTAAACTTAACCAACATATGCACAACTGACAATTCTTTTCGTGACCATGTTCTCAAATTATGGTGAAGGTGTTTGAAG[T/C]
AACCTTAACCTGGTCGGGCTCTGTTGAACTTTTTGGTCGATGTCGAGAAACATTGCCGGCTGTAGTTTTTTGGAGGTAGTTAACTGGTGCGATTCACTTT

Reverse complement sequence

AAAGTGAATCGCACCAGTTAACTACCTCCAAAAAACTACAGCCGGCAATGTTTCTCGACATCGACCAAAAAGTTCAACAGAGCCCGACCAGGTTAAGGTT[A/G]
CTTCAAACACCTTCACCATAATTTGAGAACATGGTCACGAAAAGAATTGTCAGTTGTGCATATGTTGGTTAAGTTTACAGAATTTTTTATGAGCTAAAGG

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	96.20%	3.30%	0.49%	0.00%	NA
All Indica	2759	98.20%	1.60%	0.25%	0.00%	NA
All Japonica	1512	91.40%	7.50%	1.06%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	94.50%	4.70%	0.76%	0.00%	NA
Temperate Japonica	767	83.60%	14.30%	2.09%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	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
vg1102756844	T -> C	LOC_Os11g05880.1	downstream_gene_variant ; 2911.0bp to feature; MODIFIER	silent_mutation	Average:48.148; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N
vg1102756844	T -> C	LOC_Os11g05870-LOC_Os11g05880	intergenic_region ; MODIFIER	silent_mutation	Average:48.148; most accessible tissue: Minghui63 panicle, score: 64.459	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1102756844	3.63E-07	NA	Heading_date	All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652