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Detailed information for vg0604726687:

Variant ID: vg0604726687 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 4726687
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGAATAAAATTTTTATATACGTGTTCCTAGCGATCTAAAAATAAAGGCTGAAAATAAACTTCAATGAAAAAACCCTAAAATTAACTTCAAATTTAAGATT[A/G]
AAAATTTAAATTTTAGCTGATAAGTACTCCCTCCGGGTTGATAATACTTGTCGTTTTGGACAAGGGCACGTCTAAAAAAACAACTTTGACCATTATTTTC

Reverse complement sequence

GAAAATAATGGTCAAAGTTGTTTTTTTAGACGTGCCCTTGTCCAAAACGACAAGTATTATCAACCCGGAGGGAGTACTTATCAGCTAAAATTTAAATTTT[T/C]
AATCTTAAATTTGAAGTTAATTTTAGGGTTTTTTCATTGAAGTTTATTTTCAGCCTTTATTTTTAGATCGCTAGGAACACGTATATAAAAATTTTATTCA

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	84.10%	15.90%	0.02%	0.00%	NA
All Indica	2759	89.80%	10.20%	0.04%	0.00%	NA
All Japonica	1512	69.20%	30.80%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	74.10%	25.90%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	95.50%	4.40%	0.11%	0.00%	NA
Indica Intermediate	786	89.10%	10.90%	0.00%	0.00%	NA
Temperate Japonica	767	50.60%	49.40%	0.00%	0.00%	NA
Tropical Japonica	504	96.00%	4.00%	0.00%	0.00%	NA
Japonica Intermediate	241	72.20%	27.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0604726687	A -> G	LOC_Os06g09390.1	upstream_gene_variant ; 4643.0bp to feature; MODIFIER	silent_mutation	Average:51.848; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0604726687	A -> G	LOC_Os06g09390.2	upstream_gene_variant ; 4643.0bp to feature; MODIFIER	silent_mutation	Average:51.848; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0604726687	A -> G	LOC_Os06g09380-LOC_Os06g09390	intergenic_region ; MODIFIER	silent_mutation	Average:51.848; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0604726687	NA	1.30E-13	Plant_height	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
vg0604726687	NA	2.54E-16	Spikelet_length	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
vg0604726687	1.76E-07	NA	mr1115	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
vg0604726687	5.51E-06	NA	mr1115	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
vg0604726687	9.22E-06	NA	mr1137	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
vg0604726687	5.40E-06	5.82E-14	mr1137	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
vg0604726687	NA	4.41E-07	mr1183	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
vg0604726687	NA	5.21E-06	mr1330	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
vg0604726687	NA	2.50E-07	mr1503	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
vg0604726687	2.58E-08	NA	mr1611	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
vg0604726687	NA	4.13E-11	mr1617	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
vg0604726687	1.18E-08	NA	mr1920	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
vg0604726687	NA	2.11E-13	mr1137_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
vg0604726687	NA	4.48E-06	mr1182_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
vg0604726687	NA	3.43E-06	mr1330_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
vg0604726687	NA	8.29E-09	mr1617_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
vg0604726687	NA	4.69E-09	mr1709_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