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Detailed information for vg0716241220:

Variant ID: vg0716241220 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 16241220
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

GCTTTTGGACGTCTTTTTGGGAGCTTGGCGGTTTCATGTTGAGGATGGCGTTGATTTTCTCCGGGTTGGCCTGTATGCCTCTTTGAGATACCATAAATCC[A/G]
AGCAATTTCCCTGACGGTACTCCGAAGATGCACTTTTCCGGGTTTAGTTTCATCTTGAAAGCACGAATGCTTGTAAAAGTTTCTTCTAAATCCACAATCA

Reverse complement sequence

TGATTGTGGATTTAGAAGAAACTTTTACAAGCATTCGTGCTTTCAAGATGAAACTAAACCCGGAAAAGTGCATCTTCGGAGTACCGTCAGGGAAATTGCT[T/C]
GGATTTATGGTATCTCAAAGAGGCATACAGGCCAACCCGGAGAAAATCAACGCCATCCTCAACATGAAACCGCCAAGCTCCCAAAAAGACGTCCAAAAGC

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	38.30%	21.40%	4.13%	36.16%	NA
All Indica	2759	6.50%	26.20%	6.63%	60.64%	NA
All Japonica	1512	97.70%	1.10%	0.66%	0.53%	NA
Aus	269	8.20%	91.40%	0.00%	0.37%	NA
Indica I	595	5.40%	42.00%	6.39%	46.22%	NA
Indica II	465	5.80%	13.10%	7.96%	73.12%	NA
Indica III	913	3.50%	16.80%	6.79%	72.95%	NA
Indica Intermediate	786	11.30%	33.00%	5.85%	49.87%	NA
Temperate Japonica	767	96.30%	1.70%	1.30%	0.65%	NA
Tropical Japonica	504	99.60%	0.20%	0.00%	0.20%	NA
Japonica Intermediate	241	97.90%	1.20%	0.00%	0.83%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	56.70%	11.10%	2.22%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0716241220	A -> DEL	LOC_Os07g27834.1	N	frameshift_variant	Average:11.989; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0716241220	A -> G	LOC_Os07g27834.1	synonymous_variant ; p.Leu1034Leu; LOW	synonymous_codon	Average:11.989; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0716241220	NA	1.08E-06	mr1004	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
vg0716241220	2.26E-06	3.04E-07	mr1480	Ind_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
vg0716241220	NA	1.76E-08	mr1705_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