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Detailed information for vg1004415668:

Variant ID: vg1004415668 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4415668
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

ATTTTTTAAAAAAAATCCAAGCGAATTCCCACGTAGAATTTTACCCTAACTAAACCGTATAACAATAATAAGATTAAAATAACATTGACCCATTGCAATG[C/T]
ACGGGCATTTTTCTAGTCTAAACAAATTAAAAGAACATCAACAATAAGCTATACGACATGACACATGGAAAACTACATATTAGTTCATAGAGTGCATTTG

Reverse complement sequence

CAAATGCACTCTATGAACTAATATGTAGTTTTCCATGTGTCATGTCGTATAGCTTATTGTTGATGTTCTTTTAATTTGTTTAGACTAGAAAAATGCCCGT[G/A]
CATTGCAATGGGTCAATGTTATTTTAATCTTATTATTGTTATACGGTTTAGTTAGGGTAAAATTCTACGTGGGAATTCGCTTGGATTTTTTTTAAAAAAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.20%	20.80%	11.66%	7.36%	NA
All Indica	2759	42.00%	34.30%	17.91%	5.80%	NA
All Japonica	1512	86.00%	1.30%	2.78%	9.92%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	46.20%	20.20%	24.03%	9.58%	NA
Indica II	465	34.40%	48.40%	13.98%	3.23%	NA
Indica III	913	45.10%	34.50%	14.24%	6.13%	NA
Indica Intermediate	786	39.60%	36.50%	19.85%	4.07%	NA
Temperate Japonica	767	81.00%	1.00%	3.91%	14.08%	NA
Tropical Japonica	504	96.80%	0.20%	1.19%	1.79%	NA
Japonica Intermediate	241	79.70%	4.10%	2.49%	13.69%	NA
VI/Aromatic	96	59.40%	1.00%	7.29%	32.29%	NA
Intermediate	90	67.80%	15.60%	8.89%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004415668	C -> T	LOC_Os10g08170-LOC_Os10g08180	intergenic_region ; MODIFIER	silent_mutation	Average:28.117; most accessible tissue: Zhenshan97 young leaf, score: 37.172	N	N	N	N
vg1004415668	C -> DEL	N	N	silent_mutation	Average:28.117; most accessible tissue: Zhenshan97 young leaf, score: 37.172	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004415668	3.88E-06	3.88E-06	mr1237	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
vg1004415668	5.94E-07	NA	mr1241	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
vg1004415668	4.20E-06	4.20E-06	mr1973	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