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Detailed information for vg0802714869:

Variant ID: vg0802714869 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2714869
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

CCATCCGATAAGACCATAATGCTTCGGCTAAACGAATATGCTATTGCCGAGGATAATCAGAAATCTTCCTCTTAATCAATTTGATCAAGCACTTGTAGAT[G/T]
CCTCGGCCTGCCCATTAGCTTGTGCATAATGCGGTGAAGAATTCAATAATTTGATACCCATGCTATCGGAAAACTGAACAAACTCATCAGACACGAAAAT

Reverse complement sequence

ATTTTCGTGTCTGATGAGTTTGTTCAGTTTTCCGATAGCATGGGTATCAAATTATTGAATTCTTCACCGCATTATGCACAAGCTAATGGGCAGGCCGAGG[C/A]
ATCTACAAGTGCTTGATCAAATTGATTAAGAGGAAGATTTCTGATTATCCTCGGCAATAGCATATTCGTTTAGCCGAAGCATTATGGTCTTATCGGATGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.70%	39.30%	7.02%	0.00%	NA
All Indica	2759	33.30%	56.50%	10.22%	0.00%	NA
All Japonica	1512	80.70%	16.50%	2.84%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	12.30%	71.60%	16.13%	0.00%	NA
Indica II	465	19.40%	73.30%	7.31%	0.00%	NA
Indica III	913	49.80%	39.00%	11.17%	0.00%	NA
Indica Intermediate	786	38.30%	55.30%	6.36%	0.00%	NA
Temperate Japonica	767	97.70%	1.20%	1.17%	0.00%	NA
Tropical Japonica	504	54.00%	41.70%	4.37%	0.00%	NA
Japonica Intermediate	241	82.60%	12.40%	4.98%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	42.20%	50.00%	7.78%	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
vg0802714869	G -> T	LOC_Os08g05210.1	downstream_gene_variant ; 925.0bp to feature; MODIFIER	silent_mutation	Average:32.461; most accessible tissue: Zhenshan97 young leaf, score: 52.657	N	N	N	N
vg0802714869	G -> T	LOC_Os08g05220.1	intron_variant ; MODIFIER	silent_mutation	Average:32.461; most accessible tissue: Zhenshan97 young leaf, score: 52.657	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802714869	NA	7.67E-10	Heading_date	Ind_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
vg0802714869	NA	1.37E-06	mr1212	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
vg0802714869	NA	1.89E-19	mr1422	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
vg0802714869	NA	3.60E-17	mr1583	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
vg0802714869	NA	8.92E-11	mr1720	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
vg0802714869	NA	3.87E-11	mr1784	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
vg0802714869	NA	8.67E-07	mr1805	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
vg0802714869	NA	5.35E-10	mr1862	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
vg0802714869	NA	1.35E-06	mr1942	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
vg0802714869	NA	2.60E-24	mr1244_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
vg0802714869	NA	9.79E-14	mr1583_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
vg0802714869	NA	1.72E-17	mr1807_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
vg0802714869	NA	7.26E-11	mr1850_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