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Detailed information for vg0403274963:

Variant ID: vg0403274963 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3274963
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, C: 0.32, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTAGGCCAACTGATACTATGATAAGGAAAAAAAGAAGCAAAAACACATTGTTCATGAGTAATTTTGTAAGTAGGAGTTTTGTTTTGGTGGTGCGCTTT[C/T]
GATATATCATATTAGGTTACTACCGGGGCTTTGAATTTCATGTTGTGATTGTTCCTTCCTTACTCTTTACTTACTTCCCCTATCATAAAAAGAACCAAAT

Reverse complement sequence

ATTTGGTTCTTTTTATGATAGGGGAAGTAAGTAAAGAGTAAGGAAGGAACAATCACAACATGAAATTCAAAGCCCCGGTAGTAACCTAATATGATATATC[G/A]
AAAGCGCACCACCAAAACAAAACTCCTACTTACAAAATTACTCATGAACAATGTGTTTTTGCTTCTTTTTTTCCTTATCATAGTATCAGTTGGCCTAAGA

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	29.60%	3.20%	6.92%	60.30%	NA
All Indica	2759	19.60%	5.20%	10.95%	64.26%	NA
All Japonica	1512	52.40%	0.10%	0.73%	46.76%	NA
Aus	269	10.40%	1.50%	1.49%	86.62%	NA
Indica I	595	35.80%	2.50%	2.52%	59.16%	NA
Indica II	465	16.60%	5.40%	16.34%	61.72%	NA
Indica III	913	10.00%	6.10%	10.95%	72.95%	NA
Indica Intermediate	786	20.40%	6.00%	14.12%	59.54%	NA
Temperate Japonica	767	83.80%	0.10%	0.78%	15.25%	NA
Tropical Japonica	504	14.70%	0.20%	0.20%	84.92%	NA
Japonica Intermediate	241	31.10%	0.00%	1.66%	67.22%	NA
VI/Aromatic	96	9.40%	0.00%	2.08%	88.54%	NA
Intermediate	90	31.10%	2.20%	8.89%	57.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403274963	C -> DEL	N	N	silent_mutation	Average:17.979; most accessible tissue: Callus, score: 71.964	N	N	N	N
vg0403274963	C -> T	LOC_Os04g06280.1	intron_variant ; MODIFIER	silent_mutation	Average:17.979; most accessible tissue: Callus, score: 71.964	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403274963	6.22E-06	2.09E-10	mr1027_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
vg0403274963	NA	2.11E-08	mr1580_2	Ind_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
vg0403274963	NA	1.69E-09	mr1825_2	Ind_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