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Detailed information for vg0700711476:

Variant ID: vg0700711476 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 711476
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.64, G: 0.39, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:

CTATGTTAGATTCGCATAACACTCTTGTGCAGAAATTTCGTTATGCTAGAGAATGCTTGAACGAGCATGGGAATCAGCATTTGACGTTACGGCTGATGGG[G/C]
TGCAATGCAAAATCTGATGTGCAATATAATTTACCAACTAGCGGTGAACTAGCAGCGATTATAGTGGGCGATTACTCAGTAGCTGAGTATAGTTATGATA

Reverse complement sequence

TATCATAACTATACTCAGCTACTGAGTAATCGCCCACTATAATCGCTGCTAGTTCACCGCTAGTTGGTAAATTATATTGCACATCAGATTTTGCATTGCA[C/G]
CCCATCAGCCGTAACGTCAAATGCTGATTCCCATGCTCGTTCAAGCATTCTCTAGCATAACGAAATTTCTGCACAAGAGTGTTATGCGAATCTAACATAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.00%	40.10%	3.00%	8.97%	NA
All Indica	2759	22.40%	57.50%	4.93%	15.19%	NA
All Japonica	1512	98.90%	0.90%	0.20%	0.00%	NA
Aus	269	3.30%	95.50%	0.37%	0.74%	NA
Indica I	595	16.80%	56.80%	2.35%	24.03%	NA
Indica II	465	58.50%	38.70%	0.86%	1.94%	NA
Indica III	913	7.70%	66.00%	8.54%	17.74%	NA
Indica Intermediate	786	22.40%	59.20%	5.09%	13.36%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	97.20%	2.20%	0.60%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	88.50%	10.40%	1.04%	0.00%	NA
Intermediate	90	66.70%	28.90%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0700711476	G -> DEL	LOC_Os07g02230.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700711476	G -> C	LOC_Os07g02230.1	synonymous_variant ; p.Gly288Gly; LOW	synonymous_codon	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0700711476	NA	8.28E-06	mr1216	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
vg0700711476	NA	1.48E-06	mr1420	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
vg0700711476	NA	7.95E-07	mr1681	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
vg0700711476	NA	1.25E-07	mr1764	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
vg0700711476	2.72E-06	3.27E-08	mr1898	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