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Detailed information for vg0404504944:

Variant ID: vg0404504944 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4504944
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.29, others allele: 0.00, population size: 58. )

Flanking Sequence (100 bp) in Reference Genome:

AACATGCAGACGTATATACTCTCTCCGTTTCGTTTTATTTGACACCGTTGACTTTTTAGCATATGTTTGACCGCTCGTCTTATTCAAAAAATTTAAATAA[T/C]
TATTAATTCTTTTGCTATCATTTGATTCATCGTTAAATATACTTTTATGCATACGTATAGTTTTACATATTTCACCAAAGTTTTTAATAAGACGAACGGT

Reverse complement sequence

ACCGTTCGTCTTATTAAAAACTTTGGTGAAATATGTAAAACTATACGTATGCATAAAAGTATATTTAACGATGAATCAAATGATAGCAAAAGAATTAATA[A/G]
TTATTTAAATTTTTTGAATAAGACGAGCGGTCAAACATATGCTAAAAAGTCAACGGTGTCAAATAAAACGAAACGGAGAGAGTATATACGTCTGCATGTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.20%	23.40%	7.53%	23.83%	NA
All Indica	2759	53.90%	6.10%	11.16%	28.92%	NA
All Japonica	1512	31.50%	60.40%	1.72%	6.42%	NA
Aus	269	20.40%	3.00%	3.35%	73.23%	NA
Indica I	595	63.20%	6.70%	14.29%	15.80%	NA
Indica II	465	18.30%	4.90%	15.27%	61.51%	NA
Indica III	913	72.20%	6.20%	5.37%	16.21%	NA
Indica Intermediate	786	46.60%	6.00%	13.10%	34.35%	NA
Temperate Japonica	767	9.50%	90.20%	0.13%	0.13%	NA
Tropical Japonica	504	58.90%	19.20%	4.76%	17.06%	NA
Japonica Intermediate	241	44.00%	51.50%	0.41%	4.15%	NA
VI/Aromatic	96	87.50%	0.00%	4.17%	8.33%	NA
Intermediate	90	41.10%	20.00%	10.00%	28.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0404504944	T -> C	LOC_Os04g08400.1	downstream_gene_variant ; 1203.0bp to feature; MODIFIER	silent_mutation	Average:48.4; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0404504944	T -> C	LOC_Os04g08410.1	downstream_gene_variant ; 3860.0bp to feature; MODIFIER	silent_mutation	Average:48.4; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0404504944	T -> C	LOC_Os04g08400-LOC_Os04g08410	intergenic_region ; MODIFIER	silent_mutation	Average:48.4; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0404504944	T -> DEL	N	N	silent_mutation	Average:48.4; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404504944	NA	6.40E-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
vg0404504944	NA	7.23E-09	mr1194	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
vg0404504944	5.97E-06	NA	mr1698	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
vg0404504944	NA	9.76E-06	mr1329_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
vg0404504944	1.13E-06	NA	mr1549_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
vg0404504944	NA	4.19E-06	mr1566_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
vg0404504944	1.20E-06	NA	mr1698_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
vg0404504944	NA	2.34E-06	mr1698_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
vg0404504944	NA	3.61E-06	mr1730_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
vg0404504944	NA	2.15E-07	mr1743_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
vg0404504944	3.54E-07	NA	mr1757_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
vg0404504944	NA	4.30E-11	mr1851_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
vg0404504944	NA	2.38E-07	mr1860_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
vg0404504944	NA	1.58E-07	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
vg0404504944	NA	1.87E-09	mr1905_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