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Detailed information for vg0308026693:

Variant ID: vg0308026693 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 8026693
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TTTCTCTCTCTCGACAACAATGACAGTGCTAACGGAGTGTGGCGTGGCAGAAATATAGAGGAATAATTCTTCATTAGGTTGGGGAGCAACAAGTACAAGG[G/C]
GGTTTGATAGGTAGCGCTTGAGTGCAATGAATGCCTCTTCGGCTTTCTGTGTCCATACAAATTTGTCTTGTTTCTTCAACAGAGCGAAGAAAGGTTGTCC

Reverse complement sequence

GGACAACCTTTCTTCGCTCTGTTGAAGAAACAAGACAAATTTGTATGGACACAGAAAGCCGAAGAGGCATTCATTGCACTCAAGCGCTACCTATCAAACC[C/G]
CCTTGTACTTGTTGCTCCCCAACCTAATGAAGAATTATTCCTCTATATTTCTGCCACGCCACACTCCGTTAGCACTGTCATTGTTGTCGAGAGAGAGAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.50%	41.90%	0.06%	0.57%	NA
All Indica	2759	30.30%	68.80%	0.00%	0.87%	NA
All Japonica	1512	96.60%	3.20%	0.07%	0.13%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	22.70%	75.30%	0.00%	2.02%	NA
Indica II	465	9.20%	90.30%	0.00%	0.43%	NA
Indica III	913	39.30%	60.60%	0.00%	0.11%	NA
Indica Intermediate	786	38.20%	60.70%	0.00%	1.15%	NA
Temperate Japonica	767	99.10%	0.80%	0.00%	0.13%	NA
Tropical Japonica	504	91.70%	7.90%	0.20%	0.20%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	2.10%	1.04%	0.00%	NA
Intermediate	90	65.60%	32.20%	1.11%	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
vg0308026693	G -> C	LOC_Os03g14760.1	missense_variant ; p.Pro243Arg; MODERATE	nonsynonymous_codon ; P243R	Average:15.444; most accessible tissue: Zhenshan97 flag leaf, score: 24.112	benign	0.903	DELETERIOUS	0.01
vg0308026693	G -> DEL	LOC_Os03g14760.1	N	frameshift_variant	Average:15.444; most accessible tissue: Zhenshan97 flag leaf, score: 24.112	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0308026693	1.82E-07	NA	Grain_length	Ind_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
vg0308026693	NA	1.61E-08	mr1260	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