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Detailed information for vg0506760968:

Variant ID: vg0506760968 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 6760968
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, A: 0.15, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

CAACCACCTCGGCGCGGCAGACGGGGCACGTCGAGTGCTCCCTGAGCCACACATCGACGCAGCCCCGGTGGAAGACATGCATGCATCTGGGCAGCCGCCG[C/A]
GCCGCCTCCCCGTCGGCCATCACGGCGAGGCACACCGCGCACTCCCGTTCCTCTTCCTCCTCCTCTGCTGCCCCCACCGCGCCGCCGCCGCCCTCCTCCC

Reverse complement sequence

GGGAGGAGGGCGGCGGCGGCGCGGTGGGGGCAGCAGAGGAGGAGGAAGAGGAACGGGAGTGCGCGGTGTGCCTCGCCGTGATGGCCGACGGGGAGGCGGC[G/T]
CGGCGGCTGCCCAGATGCATGCATGTCTTCCACCGGGGCTGCGTCGATGTGTGGCTCAGGGAGCACTCGACGTGCCCCGTCTGCCGCGCCGAGGTGGTTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.40%	41.50%	0.06%	0.08%	NA
All Indica	2759	87.90%	11.90%	0.07%	0.11%	NA
All Japonica	1512	4.80%	95.20%	0.00%	0.00%	NA
Aus	269	81.80%	18.20%	0.00%	0.00%	NA
Indica I	595	98.30%	1.70%	0.00%	0.00%	NA
Indica II	465	77.40%	22.40%	0.00%	0.22%	NA
Indica III	913	85.50%	14.50%	0.00%	0.00%	NA
Indica Intermediate	786	89.10%	10.40%	0.25%	0.25%	NA
Temperate Japonica	767	1.60%	98.40%	0.00%	0.00%	NA
Tropical Japonica	504	5.20%	94.80%	0.00%	0.00%	NA
Japonica Intermediate	241	14.10%	85.90%	0.00%	0.00%	NA
VI/Aromatic	96	5.20%	94.80%	0.00%	0.00%	NA
Intermediate	90	38.90%	58.90%	1.11%	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
vg0506760968	C -> DEL	LOC_Os05g11860.1	N	frameshift_variant	Average:79.189; most accessible tissue: Zhenshan97 young leaf, score: 87.153	N	N	N	N
vg0506760968	C -> A	LOC_Os05g11860.1	synonymous_variant ; p.Ala178Ala; LOW	synonymous_codon	Average:79.189; most accessible tissue: Zhenshan97 young leaf, score: 87.153	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0506760968	NA	1.72E-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
vg0506760968	NA	9.33E-10	mr1514	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
vg0506760968	NA	4.22E-32	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
vg0506760968	NA	2.82E-42	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
vg0506760968	NA	6.09E-28	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
vg0506760968	NA	3.01E-40	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
vg0506760968	NA	8.05E-12	mr1722_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
vg0506760968	NA	3.27E-07	mr1748_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
vg0506760968	NA	3.81E-32	mr1873_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