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Detailed information for vg0906274104:

Variant ID: vg0906274104 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6274104
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

GTCAGGTAGTTACGACACGTCATTGATGACTCATCTGTGACGGGTGACAGGTTTTAACCCGTCAGAGATGACTTATATACCGGTCAGAGATGAGTTATCT[G/A]
TGATGGGTGTTTCACTCGTCACAGGTGATTTTGTCATCAGTGACCACTAATCACTAACCAAGACCAAACCCGTCAAAGGTGAGGGTTTGGGCCCGTCAGA

Reverse complement sequence

TCTGACGGGCCCAAACCCTCACCTTTGACGGGTTTGGTCTTGGTTAGTGATTAGTGGTCACTGATGACAAAATCACCTGTGACGAGTGAAACACCCATCA[C/T]
AGATAACTCATCTCTGACCGGTATATAAGTCATCTCTGACGGGTTAAAACCTGTCACCCGTCACAGATGAGTCATCAATGACGTGTCGTAACTACCTGAC

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	58.80%	5.90%	1.18%	34.13%	NA
All Indica	2759	45.80%	5.30%	0.58%	48.39%	NA
All Japonica	1512	73.90%	8.10%	2.38%	15.61%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	23.20%	12.30%	0.84%	63.70%	NA
Indica II	465	71.00%	0.20%	0.00%	28.82%	NA
Indica III	913	39.90%	3.60%	0.77%	55.75%	NA
Indica Intermediate	786	54.80%	4.80%	0.51%	39.82%	NA
Temperate Japonica	767	84.40%	5.00%	1.17%	9.52%	NA
Tropical Japonica	504	71.40%	13.90%	1.39%	13.29%	NA
Japonica Intermediate	241	45.60%	6.20%	8.30%	39.83%	NA
VI/Aromatic	96	65.60%	7.30%	2.08%	25.00%	NA
Intermediate	90	76.70%	3.30%	2.22%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906274104	G -> DEL	LOC_Os09g11300.1	N	frameshift_variant	Average:20.712; most accessible tissue: Minghui63 young leaf, score: 45.896	N	N	N	N
vg0906274104	G -> A	LOC_Os09g11300.1	missense_variant ; p.Val49Met; MODERATE	nonsynonymous_codon ; V49M	Average:20.712; most accessible tissue: Minghui63 young leaf, score: 45.896	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906274104	8.22E-07	4.15E-07	mr1768_2	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