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Detailed information for vg0506760956:

Variant ID: vg0506760956 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6760956
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.07, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

CGGCCGGCCTAACAACCACCTCGGCGCGGCAGACGGGGCACGTCGAGTGCTCCCTGAGCCACACATCGACGCAGCCCCGGTGGAAGACATGCATGCATCT[G/A]
GGCAGCCGCCGCGCCGCCTCCCCGTCGGCCATCACGGCGAGGCACACCGCGCACTCCCGTTCCTCTTCCTCCTCCTCTGCTGCCCCCACCGCGCCGCCGC

Reverse complement sequence

GCGGCGGCGCGGTGGGGGCAGCAGAGGAGGAGGAAGAGGAACGGGAGTGCGCGGTGTGCCTCGCCGTGATGGCCGACGGGGAGGCGGCGCGGCGGCTGCC[C/T]
AGATGCATGCATGTCTTCCACCGGGGCTGCGTCGATGTGTGGCTCAGGGAGCACTCGACGTGCCCCGTCTGCCGCGCCGAGGTGGTTGTTAGGCCGGCCG

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	52.10%	47.70%	0.15%	0.08%	NA
All Indica	2759	83.30%	16.40%	0.18%	0.11%	NA
All Japonica	1512	4.60%	95.30%	0.13%	0.00%	NA
Aus	269	23.80%	76.20%	0.00%	0.00%	NA
Indica I	595	96.00%	4.00%	0.00%	0.00%	NA
Indica II	465	74.20%	25.60%	0.00%	0.22%	NA
Indica III	913	84.10%	15.80%	0.11%	0.00%	NA
Indica Intermediate	786	78.20%	21.00%	0.51%	0.25%	NA
Temperate Japonica	767	1.60%	98.40%	0.00%	0.00%	NA
Tropical Japonica	504	5.20%	94.60%	0.20%	0.00%	NA
Japonica Intermediate	241	12.90%	86.70%	0.41%	0.00%	NA
VI/Aromatic	96	0.00%	100.00%	0.00%	0.00%	NA
Intermediate	90	32.20%	66.70%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0506760956	G -> DEL	LOC_Os05g11860.1	N	frameshift_variant	Average:79.968; most accessible tissue: Zhenshan97 young leaf, score: 87.993	N	N	N	N
vg0506760956	G -> A	LOC_Os05g11860.1	synonymous_variant ; p.Pro182Pro; LOW	synonymous_codon	Average:79.968; most accessible tissue: Zhenshan97 young leaf, score: 87.993	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506760956	NA	1.86E-26	mr1039	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
vg0506760956	NA	1.34E-13	mr1329	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
vg0506760956	NA	4.56E-10	mr1524	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
vg0506760956	NA	1.44E-27	mr1632	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
vg0506760956	NA	7.74E-06	mr1632	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
vg0506760956	8.10E-06	NA	mr1873	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
vg0506760956	NA	1.43E-30	mr1039_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
vg0506760956	7.06E-07	7.56E-19	mr1514_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
vg0506760956	1.90E-07	4.85E-38	mr1632_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
vg0506760956	NA	1.00E-08	mr1632_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