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Detailed information for vg0718139747:

Variant ID: vg0718139747 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 18139747
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

GATGGCTTGTCATGGATCAATCCAAGTTCCTCCTTATAAGCTTGTTTATGGACATGAAGCTGTTTTATCATGGGAAGTTCGAATCGGCTCCAGAAGAATA[G/T]
AATTGCAAAATGATTTGACGGCCGAAGAGCACTATAATCTTATGGCCGATGAACGGGAGGACTTGGTTCAGTCGCGATTACGAGCACTAGCAAAAGTTAC

Reverse complement sequence

GTAACTTTTGCTAGTGCTCGTAATCGCGACTGAACCAAGTCCTCCCGTTCATCGGCCATAAGATTATAGTGCTCTTCGGCCGTCAAATCATTTTGCAATT[C/A]
TATTCTTCTGGAGCCGATTCGAACTTCCCATGATAAAACAGCTTCATGTCCATAAACAAGCTTATAAGGAGGAACTTGGATTGATCCATGACAAGCCATC

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	85.20%	9.00%	0.78%	5.08%	NA
All Indica	2759	93.30%	4.60%	0.54%	1.56%	NA
All Japonica	1512	78.80%	11.50%	0.99%	8.73%	NA
Aus	269	34.90%	41.30%	2.60%	21.19%	NA
Indica I	595	98.80%	1.00%	0.00%	0.17%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	90.10%	5.60%	0.99%	3.29%	NA
Indica Intermediate	786	89.10%	8.70%	0.76%	1.53%	NA
Temperate Japonica	767	97.30%	1.80%	0.00%	0.91%	NA
Tropical Japonica	504	53.60%	24.80%	1.79%	19.84%	NA
Japonica Intermediate	241	72.60%	14.50%	2.49%	10.37%	NA
VI/Aromatic	96	92.70%	5.20%	0.00%	2.08%	NA
Intermediate	90	84.40%	8.90%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0718139747	G -> DEL	LOC_Os07g30650.1	N	frameshift_variant	Average:34.728; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg0718139747	G -> T	LOC_Os07g30650.1	stop_gained ; p.Glu742*; HIGH	stop_gained	Average:34.728; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0718139747	4.52E-07	NA	mr1006_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
vg0718139747	NA	1.92E-07	mr1498_2	Jap_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