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Detailed information for vg0315261472:

Variant ID: vg0315261472 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15261472
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.54, C: 0.46, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

TGCGTCGTGGGTTGGTCGAGAACAACATGAAGATCCTGGAGCTGCGACAGGAGAATCTGCAGCTGAAGAGGACCTAGACGCAGTGGAGGCGCAGCTGTGT[T/C]
AGCTCAAGATCGCCCAGGGAGAGGTCTGTCGCCCCAAGCGCCGCCGCGTCTGCCGCAGCCTGAAGATCACCGCCCGCAAGAGTACCTCCAGGCCCGAGCT

Reverse complement sequence

AGCTCGGGCCTGGAGGTACTCTTGCGGGCGGTGATCTTCAGGCTGCGGCAGACGCGGCGGCGCTTGGGGCGACAGACCTCTCCCTGGGCGATCTTGAGCT[A/G]
ACACAGCTGCGCCTCCACTGCGTCTAGGTCCTCTTCAGCTGCAGATTCTCCTGTCGCAGCTCCAGGATCTTCATGTTGTTCTCGACCAACCCACGACGCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.80%	29.90%	9.86%	0.42%	NA
All Indica	2759	36.00%	49.80%	14.24%	0.00%	NA
All Japonica	1512	95.20%	0.30%	3.17%	1.32%	NA
Aus	269	84.00%	8.90%	7.06%	0.00%	NA
Indica I	595	58.20%	30.40%	11.43%	0.00%	NA
Indica II	465	34.60%	53.10%	12.26%	0.00%	NA
Indica III	913	18.30%	62.90%	18.84%	0.00%	NA
Indica Intermediate	786	40.60%	47.20%	12.21%	0.00%	NA
Temperate Japonica	767	97.00%	0.30%	1.56%	1.17%	NA
Tropical Japonica	504	96.40%	0.20%	2.98%	0.40%	NA
Japonica Intermediate	241	86.70%	0.80%	8.71%	3.73%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	82.20%	13.30%	4.44%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0315261472	T -> C	LOC_Os03g26750.1	intron_variant ; MODIFIER	silent_mutation	Average:54.236; most accessible tissue: Minghui63 flag leaf, score: 80.241	N	N	N	N
vg0315261472	T -> DEL	N	N	silent_mutation	Average:54.236; most accessible tissue: Minghui63 flag leaf, score: 80.241	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315261472	NA	2.13E-07	mr1040	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
vg0315261472	NA	4.66E-22	mr1077	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
vg0315261472	NA	8.81E-07	mr1502	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
vg0315261472	NA	1.33E-20	mr1541	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
vg0315261472	NA	2.81E-30	mr1737	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
vg0315261472	NA	4.13E-06	mr1780	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
vg0315261472	NA	4.85E-09	mr1804	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
vg0315261472	NA	1.46E-14	mr1982	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
vg0315261472	NA	2.39E-06	mr1020_2	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
vg0315261472	NA	4.26E-07	mr1422_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
vg0315261472	NA	4.06E-11	mr1533_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
vg0315261472	NA	5.82E-06	mr1583_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
vg0315261472	NA	1.27E-06	mr1606_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