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Detailed information for vg0906841774:

Variant ID: vg0906841774 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6841774
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

TAGAATGTGTACCCATTGATTTCATATCCTTGGATTGTCGTGATCGAGCCAGATGGTCCCCTCGCTAGGAAGGCTGGTTGTTGGTTAATCGTCTCGTTAC[C/G]
CATGAGATGTTGTCGCAGCCAAGCGGAGAAAGTATCAATGTGATGCCGTGTAATCCATGCATCGGACTTACCGATGTTTCTGGCACGAACTAGAGCCAAG

Reverse complement sequence

CTTGGCTCTAGTTCGTGCCAGAAACATCGGTAAGTCCGATGCATGGATTACACGGCATCACATTGATACTTTCTCCGCTTGGCTGCGACAACATCTCATG[G/C]
GTAACGAGACGATTAACCAACAACCAGCCTTCCTAGCGAGGGGACCATCTGGCTCGATCACGACAATCCAAGGATATGAAATCAATGGGTACACATTCTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.80%	3.80%	0.42%	2.94%	NA
All Indica	2759	94.20%	0.40%	0.65%	4.75%	NA
All Japonica	1512	89.00%	10.90%	0.00%	0.13%	NA
Aus	269	97.40%	0.00%	0.74%	1.86%	NA
Indica I	595	96.80%	0.00%	0.50%	2.69%	NA
Indica II	465	99.10%	0.00%	0.00%	0.86%	NA
Indica III	913	89.60%	0.40%	1.31%	8.65%	NA
Indica Intermediate	786	94.70%	0.90%	0.38%	4.07%	NA
Temperate Japonica	767	96.70%	3.30%	0.00%	0.00%	NA
Tropical Japonica	504	86.90%	12.70%	0.00%	0.40%	NA
Japonica Intermediate	241	68.50%	31.50%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	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
vg0906841774	C -> G	LOC_Os09g12100.1	upstream_gene_variant ; 3706.0bp to feature; MODIFIER	silent_mutation	Average:39.141; most accessible tissue: Minghui63 young leaf, score: 66.656	N	N	N	N
vg0906841774	C -> G	LOC_Os09g12110.1	intron_variant ; MODIFIER	silent_mutation	Average:39.141; most accessible tissue: Minghui63 young leaf, score: 66.656	N	N	N	N
vg0906841774	C -> DEL	N	N	silent_mutation	Average:39.141; most accessible tissue: Minghui63 young leaf, score: 66.656	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906841774	NA	2.79E-06	mr1646_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