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Detailed information for vg0604317901:

Variant ID: vg0604317901 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 4317901
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

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

Flanking Sequence (100 bp) in Reference Genome:

TGAAGATTCTCCGAGCTTCAGAAATGCTTCCACATTTTGCATACATGTCGATGAGCGCTGTCATGACATAGACATTGGGCTCCAAGTCCTCCTCAGTGAT[A/G]
ATCCTGTGCAGCCACTTCCCCAGGGACAAAGCTCCAAGCTGTGCACATGCGGAAAGAGTGCTTGAGATTGTGATTGGATTCGGTCGCACATTAAGCTTCA

Reverse complement sequence

TGAAGCTTAATGTGCGACCGAATCCAATCACAATCTCAAGCACTCTTTCCGCATGTGCACAGCTTGGAGCTTTGTCCCTGGGGAAGTGGCTGCACAGGAT[T/C]
ATCACTGAGGAGGACTTGGAGCCCAATGTCTATGTCATGACAGCGCTCATCGACATGTATGCAAAATGTGGAAGCATTTCTGAAGCTCGGAGAATCTTCA

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	89.50%	10.50%	0.02%	0.00%	NA
All Indica	2759	94.80%	5.20%	0.04%	0.00%	NA
All Japonica	1512	78.00%	22.00%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	88.60%	11.40%	0.00%	0.00%	NA
Indica III	913	96.80%	3.10%	0.11%	0.00%	NA
Indica Intermediate	786	92.20%	7.80%	0.00%	0.00%	NA
Temperate Japonica	767	67.80%	32.20%	0.00%	0.00%	NA
Tropical Japonica	504	93.80%	6.20%	0.00%	0.00%	NA
Japonica Intermediate	241	77.60%	22.40%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0604317901	A -> G	LOC_Os06g08660.1	synonymous_variant ; p.Ile439Ile; LOW	nonsynonymous_codon ; I439V	Average:63.4; most accessible tissue: Minghui63 flag leaf, score: 81.312	benign	0.239	TOLERATED	0.08

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0604317901	NA	7.06E-11	Awn_length	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
vg0604317901	4.12E-11	NA	mr1137	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
vg0604317901	1.73E-09	4.30E-09	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
vg0604317901	NA	3.38E-06	mr1201	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
vg0604317901	NA	3.92E-06	mr1274	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
vg0604317901	3.04E-06	NA	mr1334	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
vg0604317901	NA	1.94E-06	mr1382	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
vg0604317901	5.29E-10	NA	mr1617	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
vg0604317901	7.40E-09	3.14E-09	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
vg0604317901	NA	9.44E-06	mr1707	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
vg0604317901	4.49E-13	NA	mr1137_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
vg0604317901	4.13E-09	2.15E-10	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
vg0604317901	1.24E-06	NA	mr1617_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
vg0604317901	NA	1.61E-06	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