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Detailed information for vg0628126153:

Variant ID: vg0628126153 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 28126153
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, A: 0.27, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

CCACGTGGATCGAAGAATCGGTCAATATTGCGACGTAGGCGCCACGTCAGCAAAATCGCCTCCCAAAACCGCGCAGGGAGTCAAATTGCACTGGTTTTAG[A/G]
AGTTTGGGGGTCGAGATATCTGGTTTTGTGGTTTAGGGTTATGGATTAGATTTTGATCACAGTTGAGGGTCATGAAGTGAACTTATTCCTTCTAATGGGC

Reverse complement sequence

GCCCATTAGAAGGAATAAGTTCACTTCATGACCCTCAACTGTGATCAAAATCTAATCCATAACCCTAAACCACAAAACCAGATATCTCGACCCCCAAACT[T/C]
CTAAAACCAGTGCAATTTGACTCCCTGCGCGGTTTTGGGAGGCGATTTTGCTGACGTGGCGCCTACGTCGCAATATTGACCGATTCTTCGATCCACGTGG

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	54.60%	35.10%	5.16%	5.14%	NA
All Indica	2759	83.50%	2.90%	5.11%	8.45%	NA
All Japonica	1512	2.80%	96.30%	0.73%	0.20%	NA
Aus	269	65.80%	27.90%	5.95%	0.37%	NA
Indica I	595	81.50%	4.20%	6.22%	8.07%	NA
Indica II	465	77.60%	2.20%	9.03%	11.18%	NA
Indica III	913	90.50%	0.30%	2.30%	6.90%	NA
Indica Intermediate	786	80.50%	5.30%	5.22%	8.91%	NA
Temperate Japonica	767	2.90%	96.30%	0.52%	0.26%	NA
Tropical Japonica	504	2.80%	97.20%	0.00%	0.00%	NA
Japonica Intermediate	241	2.50%	94.20%	2.90%	0.41%	NA
VI/Aromatic	96	10.40%	19.80%	69.79%	0.00%	NA
Intermediate	90	52.20%	31.10%	10.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0628126153	A -> G	LOC_Os06g46360.1	downstream_gene_variant ; 2919.0bp to feature; MODIFIER	silent_mutation	Average:59.95; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg0628126153	A -> G	LOC_Os06g46350-LOC_Os06g46360	intergenic_region ; MODIFIER	silent_mutation	Average:59.95; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N
vg0628126153	A -> DEL	N	N	silent_mutation	Average:59.95; most accessible tissue: Minghui63 panicle, score: 84.552	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0628126153	NA	3.55E-09	mr1379_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
vg0628126153	4.28E-06	4.28E-06	mr1781_2	Ind_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