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Detailed information for vg0104403637:

Variant ID: vg0104403637 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 4403637
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.53, G: 0.47, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTAACTTTTTCCTTTTGTTTTTTATTTTCCTATGCGTAAGGGTAAATTGGACAAATCATATAGATTTTGCATGAATGATGACATGGCATGTCCATGTG[G/A]
CGATTTTGGTGGGACCAAGGACTATATCAGTCCACATGATAAATTTAAAGGACTTGTTTGGACAATATAAAATATTAAGGACTAAAATGATCCAGGAGCG

Reverse complement sequence

CGCTCCTGGATCATTTTAGTCCTTAATATTTTATATTGTCCAAACAAGTCCTTTAAATTTATCATGTGGACTGATATAGTCCTTGGTCCCACCAAAATCG[C/T]
CACATGGACATGCCATGTCATCATTCATGCAAAATCTATATGATTTGTCCAATTTACCCTTACGCATAGGAAAATAAAAAACAAAAGGAAAAAGTTAAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.60%	19.20%	15.21%	5.97%	NA
All Indica	2759	64.80%	1.20%	24.14%	9.86%	NA
All Japonica	1512	44.50%	54.90%	0.53%	0.07%	NA
Aus	269	91.10%	3.00%	4.46%	1.49%	NA
Indica I	595	61.20%	0.20%	32.44%	6.22%	NA
Indica II	465	50.30%	1.70%	33.98%	13.98%	NA
Indica III	913	69.30%	1.00%	17.74%	11.94%	NA
Indica Intermediate	786	70.70%	2.00%	19.47%	7.76%	NA
Temperate Japonica	767	9.50%	89.70%	0.78%	0.00%	NA
Tropical Japonica	504	96.20%	3.40%	0.40%	0.00%	NA
Japonica Intermediate	241	47.70%	51.90%	0.00%	0.41%	NA
VI/Aromatic	96	61.50%	19.80%	15.62%	3.12%	NA
Intermediate	90	61.10%	16.70%	20.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0104403637	G -> A	LOC_Os01g08770.1	downstream_gene_variant ; 1556.0bp to feature; MODIFIER	silent_mutation	Average:38.363; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0104403637	G -> A	LOC_Os01g08780.1	intron_variant ; MODIFIER	silent_mutation	Average:38.363; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N
vg0104403637	G -> DEL	N	N	silent_mutation	Average:38.363; most accessible tissue: Zhenshan97 panicle, score: 61.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0104403637	NA	4.40E-13	Grain_thickness	Jap_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
vg0104403637	NA	1.07E-19	mr1308	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
vg0104403637	NA	1.03E-06	mr1308	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
vg0104403637	NA	7.74E-08	mr1364	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
vg0104403637	NA	5.71E-11	mr1368	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
vg0104403637	NA	2.08E-15	mr1401	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
vg0104403637	NA	8.41E-08	mr1443	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
vg0104403637	NA	6.62E-07	mr1443	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
vg0104403637	NA	5.57E-10	mr1575	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
vg0104403637	NA	5.70E-24	mr1584	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
vg0104403637	NA	1.15E-07	mr1584	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
vg0104403637	NA	3.71E-07	mr1606	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
vg0104403637	NA	3.32E-06	mr1657	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
vg0104403637	NA	1.19E-16	mr1830	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
vg0104403637	NA	4.07E-06	mr1884	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
vg0104403637	NA	6.18E-18	mr1156_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
vg0104403637	NA	2.73E-06	mr1268_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
vg0104403637	NA	1.97E-08	mr1364_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
vg0104403637	NA	1.04E-09	mr1825_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
vg0104403637	NA	6.88E-08	mr1952_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