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Detailed information for vg1004557426:

Variant ID: vg1004557426 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4557426
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

TGGACGGAGGTGTCGCACTCTGCTCTTCTGGGATCAGACAGGGCAACGCCAGTTGTTTGGTACAGAAGTTTTAAATGAGGCAGAAGAGAAAGTCAGAGCT[G/A]
CCAGGGAAAGATTAAGAATAGCGCAATCTCGACAGAAAAGCTGTGCAGACAACCGCCGAAGGGAGCTCGCTTTCGAAGCAGGGGATTATGTGTATCTCTG

Reverse complement sequence

CAGAGATACACATAATCCCCTGCTTCGAAAGCGAGCTCCCTTCGGCGGTTGTCTGCACAGCTTTTCTGTCGAGATTGCGCTATTCTTAATCTTTCCCTGG[C/T]
AGCTCTGACTTTCTCTTCTGCCTCATTTAAAACTTCTGTACCAAACAACTGGCGTTGCCCTGTCTGATCCCAGAAGAGCAGAGTGCGACACCTCCGTCCA

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	59.00%	24.40%	3.43%	13.18%	NA
All Indica	2759	44.50%	40.30%	1.59%	13.59%	NA
All Japonica	1512	92.10%	0.80%	4.17%	2.91%	NA
Aus	269	11.20%	2.60%	17.47%	68.77%	NA
Indica I	595	20.30%	40.70%	2.69%	36.30%	NA
Indica II	465	42.80%	47.30%	1.51%	8.39%	NA
Indica III	913	55.20%	40.40%	0.66%	3.72%	NA
Indica Intermediate	786	51.30%	35.90%	1.91%	10.94%	NA
Temperate Japonica	767	99.20%	0.70%	0.13%	0.00%	NA
Tropical Japonica	504	80.40%	0.00%	11.51%	8.13%	NA
Japonica Intermediate	241	94.20%	2.90%	1.66%	1.24%	NA
VI/Aromatic	96	84.40%	1.00%	3.12%	11.46%	NA
Intermediate	90	63.30%	22.20%	5.56%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004557426	G -> A	LOC_Os10g08390.1	missense_variant ; p.Ala736Thr; MODERATE	nonsynonymous_codon ; A736T	Average:35.801; most accessible tissue: Minghui63 flag leaf, score: 60.569	benign	0.344	DELETERIOUS	0.00
vg1004557426	G -> DEL	LOC_Os10g08390.1	N	frameshift_variant	Average:35.801; most accessible tissue: Minghui63 flag leaf, score: 60.569	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004557426	4.35E-06	3.31E-09	mr1053_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
vg1004557426	NA	2.91E-06	mr1053_2	Ind_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
vg1004557426	4.02E-06	4.00E-06	mr1058_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
vg1004557426	8.74E-06	NA	mr1220_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
vg1004557426	NA	1.07E-06	mr1250_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
vg1004557426	NA	4.84E-06	mr1308_2	Ind_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
vg1004557426	6.91E-06	6.91E-06	mr1433_2	Ind_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
vg1004557426	NA	9.76E-06	mr1603_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
vg1004557426	NA	8.58E-06	mr1603_2	Ind_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
vg1004557426	NA	4.63E-07	mr1691_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
vg1004557426	NA	3.00E-06	mr1691_2	Ind_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
vg1004557426	NA	5.65E-06	mr1729_2	Ind_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
vg1004557426	3.58E-06	7.92E-08	mr1852_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
vg1004557426	NA	4.04E-06	mr1901_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