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Detailed information for vg0307948436:

Variant ID: vg0307948436 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 7948436
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

GGCTAGTAAAAATGGGGGCACCGTGACATCCTGACCGAATTAATTTGAATTTAGTTTGTATGGACAATAAATACTGTGTACGCATATTTAGTATCACATG[C/T]
CATTTAAATAAGAGCGAAATCAACTTATAAGGACTTTTCTCTCCAACCATATTAAGTAGTGTAGTATGTGTGAGTGGATCCGCCCATCGGATGAGCATAT

Reverse complement sequence

ATATGCTCATCCGATGGGCGGATCCACTCACACATACTACACTACTTAATATGGTTGGAGAGAAAAGTCCTTATAAGTTGATTTCGCTCTTATTTAAATG[G/A]
CATGTGATACTAAATATGCGTACACAGTATTTATTGTCCATACAAACTAAATTCAAATTAATTCGGTCAGGATGTCACGGTGCCCCCATTTTTACTAGCC

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	91.90%	7.50%	0.57%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	75.30%	22.90%	1.79%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	93.60%	5.30%	1.04%	0.00%	NA
Tropical Japonica	504	68.10%	30.80%	1.19%	0.00%	NA
Japonica Intermediate	241	32.40%	62.20%	5.39%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	0.00%	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
vg0307948436	C -> T	LOC_Os03g14630.1	upstream_gene_variant ; 1256.0bp to feature; MODIFIER	silent_mutation	Average:67.108; most accessible tissue: Zhenshan97 young leaf, score: 83.831	N	N	N	N
vg0307948436	C -> T	LOC_Os03g14630-LOC_Os03g14642	intergenic_region ; MODIFIER	silent_mutation	Average:67.108; most accessible tissue: Zhenshan97 young leaf, score: 83.831	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0307948436	NA	1.39E-11	Grain_weight	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
vg0307948436	NA	2.00E-12	mr1871	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
vg0307948436	NA	5.91E-06	mr1114_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
vg0307948436	6.90E-06	NA	mr1120_2	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
vg0307948436	NA	6.11E-07	mr1120_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
vg0307948436	1.33E-06	NA	mr1238_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
vg0307948436	NA	6.49E-07	mr1247_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
vg0307948436	1.06E-06	NA	mr1484_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
vg0307948436	NA	6.54E-09	mr1554_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
vg0307948436	NA	1.66E-07	mr1566_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
vg0307948436	NA	9.32E-06	mr1566_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
vg0307948436	NA	1.36E-06	mr1691_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
vg0307948436	NA	9.95E-07	mr1730_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
vg0307948436	NA	1.91E-10	mr1905_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