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Detailed information for vg0402649721:

Variant ID: vg0402649721 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2649721
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.03, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

CGGCGAGCTTGGCGTTGAAATTTTCATCCAAGAGTACATTGCCTGGTTTGATGTCTCTATGCAGGATATGTGGGTCGCACTCGTGATGTAGGTAGAGCAG[A/G]
CCCGATCTAATGTCCTTGGCTATTTTGTACCTGTTTGATCGATCATGGTTAGATAAATACATAGATTGACTATAAACATTCTTAGTTAATTTAATGCCAA

Reverse complement sequence

TTGGCATTAAATTAACTAAGAATGTTTATAGTCAATCTATGTATTTATCTAACCATGATCGATCAAACAGGTACAAAATAGCCAAGGACATTAGATCGGG[T/C]
CTGCTCTACCTACATCACGAGTGCGACCCACATATCCTGCATAGAGACATCAAACCAGGCAATGTACTCTTGGATGAAAATTTCAACGCCAAGCTCGCCG

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	41.60%	28.70%	1.63%	28.10%	NA
All Indica	2759	23.80%	46.80%	1.96%	27.44%	NA
All Japonica	1512	62.20%	2.00%	1.19%	34.66%	NA
Aus	269	91.40%	0.70%	0.37%	7.43%	NA
Indica I	595	4.40%	90.10%	0.00%	5.55%	NA
Indica II	465	14.60%	54.00%	5.16%	26.24%	NA
Indica III	913	43.90%	18.60%	0.88%	36.58%	NA
Indica Intermediate	786	20.70%	42.40%	2.80%	34.10%	NA
Temperate Japonica	767	86.80%	1.30%	0.78%	11.08%	NA
Tropical Japonica	504	37.50%	1.80%	1.39%	59.33%	NA
Japonica Intermediate	241	35.30%	4.60%	2.07%	58.09%	NA
VI/Aromatic	96	88.50%	3.10%	1.04%	7.29%	NA
Intermediate	90	38.90%	35.60%	3.33%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402649721	A -> DEL	LOC_Os04g05330.1	N	frameshift_variant	Average:27.794; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N
vg0402649721	A -> G	LOC_Os04g05330.1	synonymous_variant ; p.Gly442Gly; LOW	synonymous_codon	Average:27.794; most accessible tissue: Zhenshan97 flag leaf, score: 56.01	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402649721	1.53E-06	NA	mr1193_2	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