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Detailed information for vg0114526720:

Variant ID: vg0114526720 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14526720
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

GAATAGTTCTGCAAATAAGAAACACATGATCAAAACTAGAAAAGAAGCACAAAATGAAACCAGACATCTAGGAACAAGCGGTTGAACCGTTGAAGATTCA[C/A]
CAAATCGAGAATATGGCATCTCTACCAAATCGACAATATAGCATCTCCAAGGCTTCGAGATAGTACTAGATAATAAATCTGCTTTCCAGGTCGTGTTGAT

Reverse complement sequence

ATCAACACGACCTGGAAAGCAGATTTATTATCTAGTACTATCTCGAAGCCTTGGAGATGCTATATTGTCGATTTGGTAGAGATGCCATATTCTCGATTTG[G/T]
TGAATCTTCAACGGTTCAACCGCTTGTTCCTAGATGTCTGGTTTCATTTTGTGCTTCTTTTCTAGTTTTGATCATGTGTTTCTTATTTGCAGAACTATTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.60%	11.20%	0.34%	3.89%	NA
All Indica	2759	76.40%	16.50%	0.58%	6.52%	NA
All Japonica	1512	97.50%	2.40%	0.00%	0.07%	NA
Aus	269	88.10%	11.20%	0.00%	0.74%	NA
Indica I	595	85.50%	9.60%	0.17%	4.71%	NA
Indica II	465	94.60%	2.40%	0.65%	2.37%	NA
Indica III	913	62.40%	29.00%	0.44%	8.11%	NA
Indica Intermediate	786	74.80%	15.60%	1.02%	8.52%	NA
Temperate Japonica	767	98.70%	1.20%	0.00%	0.13%	NA
Tropical Japonica	504	95.00%	5.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114526720	C -> A	LOC_Os01g25630.1	intron_variant ; MODIFIER	silent_mutation	Average:50.113; most accessible tissue: Zhenshan97 flower, score: 77.366	N	N	N	N
vg0114526720	C -> DEL	N	N	silent_mutation	Average:50.113; most accessible tissue: Zhenshan97 flower, score: 77.366	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114526720	NA	3.27E-07	Grain_weight	Ind_All	Not	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