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Detailed information for vg0428798409:

Variant ID: vg0428798409 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 28798409
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

AGATTAGATCTCCGGTCTGACCGCCGAGATCAGCTGCCATTCGCTATCGCCGCCGCCGGTCTGACCGCCGCCTTGCTGCCGGTCTGACCGCCGGTGAGTT[A/G]
CCGGTTAGACCGCCGAAACCCGGTGAAACACAAATCGAAGAACTCTTAAAGTAGATGACGACTTTATTGATTCTCTCTGTGTTTACAAAGTGCACCAACA

Reverse complement sequence

TGTTGGTGCACTTTGTAAACACAGAGAGAATCAATAAAGTCGTCATCTACTTTAAGAGTTCTTCGATTTGTGTTTCACCGGGTTTCGGCGGTCTAACCGG[T/C]
AACTCACCGGCGGTCAGACCGGCAGCAAGGCGGCGGTCAGACCGGCGGCGGCGATAGCGAATGGCAGCTGATCTCGGCGGTCAGACCGGAGATCTAATCT

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	52.50%	46.00%	0.30%	1.18%	NA
All Indica	2759	82.80%	14.80%	0.43%	2.03%	NA
All Japonica	1512	0.40%	99.60%	0.00%	0.00%	NA
Aus	269	56.50%	43.50%	0.00%	0.00%	NA
Indica I	595	96.10%	2.50%	0.34%	1.01%	NA
Indica II	465	92.50%	4.90%	0.22%	2.37%	NA
Indica III	913	67.30%	29.90%	0.44%	2.41%	NA
Indica Intermediate	786	85.00%	12.20%	0.64%	2.16%	NA
Temperate Japonica	767	0.10%	99.90%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.20%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.60%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	41.10%	56.70%	2.22%	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
vg0428798409	A -> DEL	N	N	silent_mutation	Average:52.344; most accessible tissue: Minghui63 flag leaf, score: 70.648	N	N	N	N
vg0428798409	A -> G	LOC_Os04g48310-LOC_Os04g48320	intergenic_region ; MODIFIER	silent_mutation	Average:52.344; most accessible tissue: Minghui63 flag leaf, score: 70.648	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0428798409	1.50E-06	3.10E-06	mr1130	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