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Detailed information for vg0908364756:

Variant ID: vg0908364756 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 8364756
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTTCTCATGACTTCTCTGAGGGGGAAGGAGGAAACAACTGTGACTCTGTGGGCTTGAAAGTAGTGGCGTAGCTTTCTTGATGTCATAATTACTGCATA[G/A]
AGCAGCTTTTGGATCTGTAGATATCTTGTCTTCGCGTCGTGGAGGGCTTCGCTGACGTAGTAGACTGGTCTTTGCACCTTCTCTCTCAACAACAATGACA

Reverse complement sequence

TGTCATTGTTGTTGAGAGAGAAGGTGCAAAGACCAGTCTACTACGTCAGCGAAGCCCTCCACGACGCGAAGACAAGATATCTACAGATCCAAAAGCTGCT[C/T]
TATGCAGTAATTATGACATCAAGAAAGCTACGCCACTACTTTCAAGCCCACAGAGTCACAGTTGTTTCCTCCTTCCCCCTCAGAGAAGTCATGAGAAACA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.40%	21.10%	10.14%	11.38%	NA
All Indica	2759	50.50%	30.60%	15.44%	3.48%	NA
All Japonica	1512	72.20%	2.40%	1.52%	23.88%	NA
Aus	269	35.70%	37.20%	8.18%	18.96%	NA
Indica I	595	54.80%	26.10%	16.97%	2.18%	NA
Indica II	465	80.00%	11.80%	7.74%	0.43%	NA
Indica III	913	27.30%	47.20%	18.07%	7.45%	NA
Indica Intermediate	786	56.60%	26.00%	15.78%	1.65%	NA
Temperate Japonica	767	96.00%	0.00%	0.78%	3.26%	NA
Tropical Japonica	504	43.50%	6.20%	2.98%	47.42%	NA
Japonica Intermediate	241	56.80%	2.10%	0.83%	40.25%	NA
VI/Aromatic	96	67.70%	3.10%	3.12%	26.04%	NA
Intermediate	90	76.70%	12.20%	5.56%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0908364756	G -> DEL	LOC_Os09g14120.1	N	frameshift_variant	Average:32.002; most accessible tissue: Minghui63 young leaf, score: 58.21	N	N	N	N
vg0908364756	G -> A	LOC_Os09g14120.1	synonymous_variant ; p.Leu960Leu; LOW	synonymous_codon	Average:32.002; most accessible tissue: Minghui63 young leaf, score: 58.21	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0908364756	4.47E-06	4.47E-06	mr1348	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