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Detailed information for vg0419773387:

Variant ID: vg0419773387 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 19773387
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.69, G: 0.30, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

GGGCGAATGTCACGTTGCGCAGATCCGGACCTCCACGACCAGATCTTGCGATGAGGCTTGCGAGCGGCAGGAAAGACAAAGGAGAGCCAGAGCTCGACGG[T/G]
GCGCATGTGGCAATGGTACAACGGTCGGTGCTGAAGGCGGTGTAAGGGACAGCCAGAGCTAGCATCCCAACGTCTAGATCCGGCATGCCCCTGACCGGAT

Reverse complement sequence

ATCCGGTCAGGGGCATGCCGGATCTAGACGTTGGGATGCTAGCTCTGGCTGTCCCTTACACCGCCTTCAGCACCGACCGTTGTACCATTGCCACATGCGC[A/C]
CCGTCGAGCTCTGGCTCTCCTTTGTCTTTCCTGCCGCTCGCAAGCCTCATCGCAAGATCTGGTCGTGGAGGTCCGGATCTGCGCAACGTGACATTCGCCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.30%	39.30%	0.17%	0.21%	NA
All Indica	2759	94.70%	4.90%	0.11%	0.25%	NA
All Japonica	1512	0.30%	99.50%	0.13%	0.07%	NA
Aus	269	67.30%	32.30%	0.37%	0.00%	NA
Indica I	595	91.60%	8.10%	0.17%	0.17%	NA
Indica II	465	93.50%	5.80%	0.00%	0.65%	NA
Indica III	913	97.70%	2.10%	0.11%	0.11%	NA
Indica Intermediate	786	94.30%	5.30%	0.13%	0.25%	NA
Temperate Japonica	767	0.40%	99.50%	0.13%	0.00%	NA
Tropical Japonica	504	0.40%	99.40%	0.00%	0.20%	NA
Japonica Intermediate	241	0.00%	99.60%	0.41%	0.00%	NA
VI/Aromatic	96	33.30%	66.70%	0.00%	0.00%	NA
Intermediate	90	21.10%	74.40%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0419773387	T -> DEL	LOC_Os04g32780.1	N	frameshift_variant	Average:59.454; most accessible tissue: Zhenshan97 young leaf, score: 83.831	N	N	N	N
vg0419773387	T -> G	LOC_Os04g32780.1	synonymous_variant ; p.Gly55Gly; LOW	synonymous_codon	Average:59.454; most accessible tissue: Zhenshan97 young leaf, score: 83.831	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0419773387	NA	1.93E-79	mr1718	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
vg0419773387	NA	7.33E-16	mr1040_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
vg0419773387	NA	2.37E-07	mr1321_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
vg0419773387	NA	5.87E-20	mr1362_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
vg0419773387	NA	2.52E-07	mr1568_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
vg0419773387	NA	2.60E-21	mr1581_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
vg0419773387	NA	1.54E-22	mr1609_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
vg0419773387	NA	1.10E-16	mr1712_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
vg0419773387	NA	1.17E-12	mr1713_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
vg0419773387	NA	1.02E-108	mr1718_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
vg0419773387	NA	1.83E-49	mr1721_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
vg0419773387	NA	6.28E-17	mr1836_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
vg0419773387	NA	2.05E-06	mr1915_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