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Detailed information for vg1117717090:

Variant ID: vg1117717090 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17717090
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, T: 0.01, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

GTTCCACCGTCCTAATGGGGAATGGGTCACATGCTTCTGTTCATGGTGTTGGCACGGTAGATCTGAAGTTTACTTTGGGAAAGATCATGTAGGTGAAGAA[C/T]
GTGCAGCATGTCCCTTCTATCGACAGGAATCTTGTTAGTGGCTCCTGTCTGACTAGAGACGGATTTAAGTTGGTTTTTGAGTCTAATAAAGTAGTCGTGT

Reverse complement sequence

ACACGACTACTTTATTAGACTCAAAAACCAACTTAAATCCGTCTCTAGTCAGACAGGAGCCACTAACAAGATTCCTGTCGATAGAAGGGACATGCTGCAC[G/A]
TTCTTCACCTACATGATCTTTCCCAAAGTAAACTTCAGATCTACCGTGCCAACACCATGAACAGAAGCATGTGACCCATTCCCCATTAGGACGGTGGAAC

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	26.90%	10.10%	50.02%	12.99%	NA
All Indica	2759	12.60%	5.40%	60.86%	21.09%	NA
All Japonica	1512	52.50%	21.30%	24.93%	1.26%	NA
Aus	269	17.80%	0.00%	79.93%	2.23%	NA
Indica I	595	8.60%	14.30%	34.29%	42.86%	NA
Indica II	465	25.20%	1.30%	58.28%	15.27%	NA
Indica III	913	8.40%	2.50%	78.64%	10.41%	NA
Indica Intermediate	786	13.10%	4.60%	61.83%	20.48%	NA
Temperate Japonica	767	58.50%	39.40%	1.43%	0.65%	NA
Tropical Japonica	504	29.40%	3.20%	65.08%	2.38%	NA
Japonica Intermediate	241	81.70%	1.70%	15.77%	0.83%	NA
VI/Aromatic	96	50.00%	2.10%	47.92%	0.00%	NA
Intermediate	90	34.40%	5.60%	52.22%	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
vg1117717090	C -> T	LOC_Os11g30484.1	upstream_gene_variant ; 4990.0bp to feature; MODIFIER	silent_mutation	Average:18.034; most accessible tissue: Minghui63 young leaf, score: 31.294	N	N	N	N
vg1117717090	C -> T	LOC_Os11g30470.1	intron_variant ; MODIFIER	silent_mutation	Average:18.034; most accessible tissue: Minghui63 young leaf, score: 31.294	N	N	N	N
vg1117717090	C -> DEL	N	N	silent_mutation	Average:18.034; most accessible tissue: Minghui63 young leaf, score: 31.294	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117717090	NA	9.61E-13	Heading_date	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1117717090	NA	2.67E-06	mr1002	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
vg1117717090	NA	8.82E-06	mr1354	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
vg1117717090	2.06E-06	1.83E-10	mr1002_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
vg1117717090	NA	1.72E-06	mr1354_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
vg1117717090	NA	6.55E-06	mr1902_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