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Detailed information for vg0906358576:

Variant ID: vg0906358576 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6358576
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

ACTATAGAAAATAATATACTCCATTTTATCGTTGTAAAATGGAGATTCAAAGGGCCCGACGGCGGGGGTTTTCGATACTGGATTCATCGACCCTCGGAAA[A/G]
TAAACGTCGCAATGCTCGACCAATATCCGCAAGCCACAGAGGACAATCTCGTCCATCTCCTGAAGGCGCAGCATTACAAGACGTTCATACTGTTGCCGTA

Reverse complement sequence

TACGGCAACAGTATGAACGTCTTGTAATGCTGCGCCTTCAGGAGATGGACGAGATTGTCCTCTGTGGCTTGCGGATATTGGTCGAGCATTGCGACGTTTA[T/C]
TTTCCGAGGGTCGATGAATCCAGTATCGAAAACCCCCGCCGTCGGGCCCTTTGAATCTCCATTTTACAACGATAAAATGGAGTATATTATTTTCTATAGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.40%	3.70%	14.49%	3.45%	NA
All Indica	2759	80.70%	4.30%	12.11%	2.86%	NA
All Japonica	1512	83.90%	2.10%	13.82%	0.20%	NA
Aus	269	33.50%	5.90%	44.98%	15.61%	NA
Indica I	595	74.30%	6.70%	15.13%	3.87%	NA
Indica II	465	79.60%	0.00%	18.49%	1.94%	NA
Indica III	913	87.80%	3.90%	6.57%	1.64%	NA
Indica Intermediate	786	78.00%	5.50%	12.47%	4.07%	NA
Temperate Japonica	767	93.10%	3.00%	3.78%	0.13%	NA
Tropical Japonica	504	84.30%	0.60%	14.88%	0.20%	NA
Japonica Intermediate	241	53.50%	2.50%	43.57%	0.41%	NA
VI/Aromatic	96	51.00%	2.10%	12.50%	34.38%	NA
Intermediate	90	78.90%	4.40%	10.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906358576	A -> G	LOC_Os09g11410.1	downstream_gene_variant ; 1727.0bp to feature; MODIFIER	silent_mutation	Average:14.755; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0906358576	A -> G	LOC_Os09g11420.1	intron_variant ; MODIFIER	silent_mutation	Average:14.755; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N
vg0906358576	A -> DEL	N	N	silent_mutation	Average:14.755; most accessible tissue: Minghui63 panicle, score: 38.588	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906358576	4.35E-06	4.35E-06	mr1389	Jap_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
vg0906358576	NA	1.68E-08	mr1038_2	Jap_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
vg0906358576	2.03E-08	2.03E-08	mr1389_2	Jap_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