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Detailed information for vg1117387081:

Variant ID: vg1117387081 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17387081
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

CGTTGGTGCCATGAGCAGTAGCCTTGCCCAAATCCAATGACCAACTGCACGGGACGCCGCAGCGGTACTTCCCCATTGCCTCCATGCTTGAAATCCCATG[G/A]
ATCAGCGGCTCTGATACCATATTTTTAGCAACCAAATCACCAAACAACAAGAATTTCACCACGAACAACTATCCAGTCAACAGTGCTGTTTTTGGAGGTG

Reverse complement sequence

CACCTCCAAAAACAGCACTGTTGACTGGATAGTTGTTCGTGGTGAAATTCTTGTTGTTTGGTGATTTGGTTGCTAAAAATATGGTATCAGAGCCGCTGAT[C/T]
CATGGGATTTCAAGCATGGAGGCAATGGGGAAGTACCGCTGCGGCGTCCCGTGCAGTTGGTCATTGGATTTGGGCAAGGCTACTGCTCATGGCACCAACG

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	77.70%	21.90%	0.19%	0.15%	NA
All Indica	2759	77.90%	21.60%	0.25%	0.25%	NA
All Japonica	1512	87.80%	12.20%	0.00%	0.00%	NA
Aus	269	13.80%	85.50%	0.74%	0.00%	NA
Indica I	595	77.60%	22.40%	0.00%	0.00%	NA
Indica II	465	78.10%	20.90%	0.43%	0.65%	NA
Indica III	913	80.90%	19.10%	0.00%	0.00%	NA
Indica Intermediate	786	74.40%	24.40%	0.64%	0.51%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	68.30%	31.70%	0.00%	0.00%	NA
Japonica Intermediate	241	92.10%	7.90%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	77.80%	22.20%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117387081	G -> A	LOC_Os11g29920.1	synonymous_variant ; p.Ile956Ile; LOW	synonymous_codon	Average:25.701; most accessible tissue: Zhenshan97 flower, score: 46.765	N	N	N	N
vg1117387081	G -> DEL	LOC_Os11g29920.1	N	frameshift_variant	Average:25.701; most accessible tissue: Zhenshan97 flower, score: 46.765	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117387081	2.39E-06	NA	mr1017	Jap_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
vg1117387081	3.39E-07	NA	mr1132_2	Jap_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
vg1117387081	5.60E-06	NA	mr1390_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
vg1117387081	2.62E-06	NA	mr1490_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