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Detailed information for vg0131772066:

Variant ID: vg0131772066 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 31772066
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TTGTGGTGGAAATTGCCCACTCGTGTTCAAGTCCCAGACTTCTTTCAGTGGTAGACAACGTACCCATCGACAGTGAGGCACTCATGGTGACTTTGTCAAT[C/A]
TCAAAATATGTCGGCCCAATCTCTCAGAGGTACTCATAGGGGGTAAAGTGTGCATGTGTGCGTTCGTAGGGGTGAGTGTGCGTGTGTTGTGAGCGCACTT

Reverse complement sequence

AAGTGCGCTCACAACACACGCACACTCACCCCTACGAACGCACACATGCACACTTTACCCCCTATGAGTACCTCTGAGAGATTGGGCCGACATATTTTGA[G/T]
ATTGACAAAGTCACCATGAGTGCCTCACTGTCGATGGGTACGTTGTCTACCACTGAAAGAAGTCTGGGACTTGAACACGAGTGGGCAATTTCCACCACAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.60%	14.60%	0.47%	1.31%	NA
All Indica	2759	99.60%	0.20%	0.04%	0.18%	NA
All Japonica	1512	56.70%	38.20%	1.39%	3.70%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.00%	0.22%	NA
Indica III	913	99.70%	0.20%	0.00%	0.11%	NA
Indica Intermediate	786	99.00%	0.50%	0.13%	0.38%	NA
Temperate Japonica	767	76.30%	23.60%	0.00%	0.13%	NA
Tropical Japonica	504	35.50%	50.20%	3.77%	10.52%	NA
Japonica Intermediate	241	38.60%	59.80%	0.83%	0.83%	NA
VI/Aromatic	96	22.90%	77.10%	0.00%	0.00%	NA
Intermediate	90	64.40%	34.40%	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
vg0131772066	C -> A	LOC_Os01g55220-LOC_Os01g55240	intergenic_region ; MODIFIER	silent_mutation	Average:44.602; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg0131772066	C -> DEL	N	N	silent_mutation	Average:44.602; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0131772066	NA	2.91E-06	mr1002	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
vg0131772066	NA	1.76E-13	mr1070	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
vg0131772066	NA	2.39E-14	mr1084	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
vg0131772066	NA	1.06E-10	mr1128	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
vg0131772066	NA	8.11E-06	mr1164	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
vg0131772066	NA	1.17E-14	mr1205	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
vg0131772066	NA	3.02E-06	mr1773	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
vg0131772066	NA	4.67E-11	mr1775	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
vg0131772066	NA	1.01E-07	mr1824	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
vg0131772066	NA	2.71E-08	mr1002_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
vg0131772066	NA	5.62E-07	mr1554_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
vg0131772066	NA	7.32E-06	mr1866_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
vg0131772066	9.47E-06	2.84E-11	mr1947_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