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Detailed information for vg0703431792:

Variant ID: vg0703431792 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 3431792
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.01, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:

ATCACATTTGAACATATCTGGGTTTTCCTTGTCATTCTTTCCATCACTAGCACACTGATTTTCAGCATTCTTTAGCACGTCCATCTCCTCGGAGCTTACA[G/A,T]
GTGATCCTAACACTTTACAAGAGGCACTTACCCTATTGACAGCGAAGTAGGGCTCTGCTAGTCTGTGAAGGCGACAAAATGAGCAGAGAAGATCTCGTGG

Reverse complement sequence

CCACGAGATCTTCTCTGCTCATTTTGTCGCCTTCACAGACTAGCAGAGCCCTACTTCGCTGTCAATAGGGTAAGTGCCTCTTGTAAAGTGTTAGGATCAC[C/T,A]
TGTAAGCTCCGAGGAGATGGACGTGCTAAAGAATGCTGAAAATCAGTGTGCTAGTGATGGAAAGAATGACAAGGAAAACCCAGATATGTTCAAATGTGAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.20%	14.50%	0.30%	0.00%	T: 0.02%
All Indica	2759	75.10%	24.50%	0.40%	0.00%	NA
All Japonica	1512	99.70%	0.10%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	23.90%	75.30%	0.84%	0.00%	NA
Indica II	465	94.00%	6.00%	0.00%	0.00%	NA
Indica III	913	95.90%	4.10%	0.00%	0.00%	NA
Indica Intermediate	786	78.60%	20.60%	0.76%	0.00%	NA
Temperate Japonica	767	99.70%	0.00%	0.26%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	6.70%	1.11%	0.00%	T: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0703431792	G -> A	LOC_Os07g06960.1	upstream_gene_variant ; 3325.0bp to feature; MODIFIER	silent_mutation	Average:46.185; most accessible tissue: Callus, score: 77.818	N	N	N	N
vg0703431792	G -> A	LOC_Os07g06980.1	downstream_gene_variant ; 4141.0bp to feature; MODIFIER	silent_mutation	Average:46.185; most accessible tissue: Callus, score: 77.818	N	N	N	N
vg0703431792	G -> A	LOC_Os07g06980.2	downstream_gene_variant ; 4141.0bp to feature; MODIFIER	silent_mutation	Average:46.185; most accessible tissue: Callus, score: 77.818	N	N	N	N
vg0703431792	G -> A	LOC_Os07g06970.1	intron_variant ; MODIFIER	silent_mutation	Average:46.185; most accessible tissue: Callus, score: 77.818	N	N	N	N
vg0703431792	G -> T	LOC_Os07g06960.1	upstream_gene_variant ; 3325.0bp to feature; MODIFIER	silent_mutation	Average:46.185; most accessible tissue: Callus, score: 77.818	N	N	N	N
vg0703431792	G -> T	LOC_Os07g06980.1	downstream_gene_variant ; 4141.0bp to feature; MODIFIER	silent_mutation	Average:46.185; most accessible tissue: Callus, score: 77.818	N	N	N	N
vg0703431792	G -> T	LOC_Os07g06980.2	downstream_gene_variant ; 4141.0bp to feature; MODIFIER	silent_mutation	Average:46.185; most accessible tissue: Callus, score: 77.818	N	N	N	N
vg0703431792	G -> T	LOC_Os07g06970.1	intron_variant ; MODIFIER	silent_mutation	Average:46.185; most accessible tissue: Callus, score: 77.818	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0703431792	NA	5.76E-12	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
vg0703431792	NA	4.33E-06	mr1170	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