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Detailed information for vg0400958004:

Variant ID: vg0400958004 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 958004
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

AATTTATCCGTTGTCCATGCATTAAGTGCAAAACCAGAGGGAGTATTCTGCAATAAGAATTATTCATATTCACTTGTTTGGGACGGGCTTCATGCCGAGC[G/A]
CTTGGACCTCACACCGGGAGCTAGGGGTTCAAATGGAAGAAGATAAAGCAGAAAACGAGAACATTCCGGACTGAGCTCAGTACGGTGGATTTGAAGTAAA

Reverse complement sequence

TTTACTTCAAATCCACCGTACTGAGCTCAGTCCGGAATGTTCTCGTTTTCTGCTTTATCTTCTTCCATTTGAACCCCTAGCTCCCGGTGTGAGGTCCAAG[C/T]
GCTCGGCATGAAGCCCGTCCCAAACAAGTGAATATGAATAATTCTTATTGCAGAATACTCCCTCTGGTTTTGCACTTAATGCATGGACAACGGATAAATT

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	83.40%	6.70%	0.17%	9.65%	NA
All Indica	2759	77.50%	6.30%	0.22%	15.98%	NA
All Japonica	1512	90.50%	9.30%	0.07%	0.20%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	88.40%	1.70%	0.00%	9.92%	NA
Indica II	465	66.50%	0.90%	0.22%	32.47%	NA
Indica III	913	81.40%	12.00%	0.33%	6.24%	NA
Indica Intermediate	786	71.10%	6.50%	0.25%	22.14%	NA
Temperate Japonica	767	83.40%	16.30%	0.13%	0.13%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	94.60%	4.60%	0.00%	0.83%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	83.30%	4.40%	1.11%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0400958004	G -> DEL	N	N	silent_mutation	Average:48.178; most accessible tissue: Zhenshan97 young leaf, score: 64.205	N	N	N	N
vg0400958004	G -> A	LOC_Os04g02560.1	downstream_gene_variant ; 1460.0bp to feature; MODIFIER	silent_mutation	Average:48.178; most accessible tissue: Zhenshan97 young leaf, score: 64.205	N	N	N	N
vg0400958004	G -> A	LOC_Os04g02550-LOC_Os04g02560	intergenic_region ; MODIFIER	silent_mutation	Average:48.178; most accessible tissue: Zhenshan97 young leaf, score: 64.205	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400958004	NA	1.52E-06	mr1094	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
vg0400958004	NA	1.98E-06	mr1111	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
vg0400958004	2.05E-06	NA	mr1305	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
vg0400958004	7.24E-06	NA	mr1585	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
vg0400958004	4.61E-06	NA	mr1586	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
vg0400958004	NA	6.18E-06	mr1751	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
vg0400958004	NA	4.32E-06	mr1798	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
vg0400958004	1.90E-08	1.92E-09	mr1928	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
vg0400958004	NA	4.59E-08	mr1970	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
vg0400958004	NA	8.52E-08	mr1973	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
vg0400958004	NA	1.31E-06	mr1094_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
vg0400958004	5.10E-06	NA	mr1305_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
vg0400958004	NA	2.68E-12	mr1798_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
vg0400958004	NA	9.12E-07	mr1970_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
vg0400958004	NA	8.11E-09	mr1973_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