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Detailed information for vg0909755639:

Variant ID: vg0909755639 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9755639
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.82, C: 0.18, others allele: 0.00, population size: 51. )

Flanking Sequence (100 bp) in Reference Genome:

AAGAAACTCACAAGAAAGTGTTAGTTCGTAATAATCTATAGATATGTAGAGCTTTTGAAGGCACTCAACACTCAAGCATATACCAAATTCTTATAATATT[C/A]
TCAAAGAATGCATAACAGGTCAATCACCATGGCTGGTTCATGGTACAATGACAAGCTTGATGAGTGGAGCGATTGCAAAGCCGGACCTGTAAAGGTTAAT

Reverse complement sequence

ATTAACCTTTACAGGTCCGGCTTTGCAATCGCTCCACTCATCAAGCTTGTCATTGTACCATGAACCAGCCATGGTGATTGACCTGTTATGCATTCTTTGA[G/T]
AATATTATAAGAATTTGGTATATGCTTGAGTGTTGAGTGCCTTCAAAAGCTCTACATATCTATAGATTATTACGAACTAACACTTTCTTGTGAGTTTCTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.70%	35.60%	0.25%	26.47%	NA
All Indica	2759	57.10%	17.50%	0.29%	25.08%	NA
All Japonica	1512	5.00%	74.40%	0.07%	20.50%	NA
Aus	269	29.40%	2.20%	0.00%	68.40%	NA
Indica I	595	81.00%	2.40%	0.50%	16.13%	NA
Indica II	465	71.40%	3.90%	0.86%	23.87%	NA
Indica III	913	32.60%	35.50%	0.11%	31.76%	NA
Indica Intermediate	786	58.90%	16.30%	0.00%	24.81%	NA
Temperate Japonica	767	1.20%	81.50%	0.13%	17.21%	NA
Tropical Japonica	504	11.10%	64.10%	0.00%	24.80%	NA
Japonica Intermediate	241	4.60%	73.40%	0.00%	21.99%	NA
VI/Aromatic	96	24.00%	30.20%	1.04%	44.79%	NA
Intermediate	90	31.10%	42.20%	2.22%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909755639	C -> DEL	N	N	silent_mutation	Average:14.948; most accessible tissue: Zhenshan97 root, score: 29.203	N	N	N	N
vg0909755639	C -> A	LOC_Os09g15950.1	upstream_gene_variant ; 4118.0bp to feature; MODIFIER	silent_mutation	Average:14.948; most accessible tissue: Zhenshan97 root, score: 29.203	N	N	N	N
vg0909755639	C -> A	LOC_Os09g15960.1	upstream_gene_variant ; 114.0bp to feature; MODIFIER	silent_mutation	Average:14.948; most accessible tissue: Zhenshan97 root, score: 29.203	N	N	N	N
vg0909755639	C -> A	LOC_Os09g15960-LOC_Os09g15970	intergenic_region ; MODIFIER	silent_mutation	Average:14.948; most accessible tissue: Zhenshan97 root, score: 29.203	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909755639	NA	3.96E-06	mr1835	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