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Detailed information for vg0517732975:

Variant ID: vg0517732975 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 17732975
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

TAGCGAGAGAAATCATCCACAACAACCAAGACATACCACTTCCCCCCAATTGACTGGACCCGAGCAGGACCAACCGTATCCATGTGAAGCAGTTATCCCG[G/A]
TCCATCTGTCATAACCATTGTAACAGGCTTGTGGGAGGAAGATGTCATTTTTCCATGACGACATGGTGCACACATAAGACCTTTCGGAGCTTTCAACTTA

Reverse complement sequence

TAAGTTGAAAGCTCCGAAAGGTCTTATGTGTGCACCATGTCGTCATGGAAAAATGACATCTTCCTCCCACAAGCCTGTTACAATGGTTATGACAGATGGA[C/T]
CGGGATAACTGCTTCACATGGATACGGTTGGTCCTGCTCGGGTCCAGTCAATTGGGGGGAAGTGGTATGTCTTGGTTGTTGTGGATGATTTCTCTCGCTA

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	78.80%	19.40%	0.91%	0.97%	NA
All Indica	2759	93.70%	5.50%	0.80%	0.00%	NA
All Japonica	1512	47.00%	48.90%	1.12%	3.04%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.20%	0.30%	1.51%	0.00%	NA
Indica II	465	74.60%	24.50%	0.86%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	95.00%	3.80%	1.15%	0.00%	NA
Temperate Japonica	767	73.00%	25.20%	0.52%	1.30%	NA
Tropical Japonica	504	17.50%	73.00%	2.58%	6.94%	NA
Japonica Intermediate	241	25.70%	73.90%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	67.80%	27.80%	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
vg0517732975	G -> DEL	LOC_Os05g30610.1	N	frameshift_variant	Average:10.009; most accessible tissue: Callus, score: 20.55	N	N	N	N
vg0517732975	G -> A	LOC_Os05g30610.1	missense_variant ; p.Thr814Ile; MODERATE	nonsynonymous_codon ; T814I	Average:10.009; most accessible tissue: Callus, score: 20.55	unknown	unknown	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0517732975	NA	5.46E-12	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
vg0517732975	NA	3.13E-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
vg0517732975	NA	7.53E-10	mr1039	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
vg0517732975	NA	2.49E-06	mr1399	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
vg0517732975	NA	4.41E-07	mr1632	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
vg0517732975	NA	3.47E-08	mr1002_2	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
vg0517732975	NA	6.24E-10	mr1039_2	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
vg0517732975	NA	3.15E-07	mr1167_2	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
vg0517732975	4.86E-07	4.86E-07	mr1181_2	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
vg0517732975	5.20E-06	5.17E-06	mr1197_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
vg0517732975	NA	6.12E-07	mr1363_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
vg0517732975	NA	7.80E-06	mr1399_2	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
vg0517732975	NA	9.28E-08	mr1582_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