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Detailed information for vg0403778987:

Variant ID: vg0403778987 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 3778987
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

GAAAGTACTGGCTCTATGGTTCATTTAAGCAAACTTGACACCACGTCAACTTTGATTAAAGCAGGCTATTTATCCTAAGCATCATGCTCAATTTAAAAAA[C/T]
CTATGAATGTCGACGACCACCCAAACCATAGCATACGAAAATGGACCGAGGACGCATAACTATGCATGATCAAGCCAGACTCAACTAGAGATAAGTATGA

Reverse complement sequence

TCATACTTATCTCTAGTTGAGTCTGGCTTGATCATGCATAGTTATGCGTCCTCGGTCCATTTTCGTATGCTATGGTTTGGGTGGTCGTCGACATTCATAG[G/A]
TTTTTTAAATTGAGCATGATGCTTAGGATAAATAGCCTGCTTTAATCAAAGTTGACGTGGTGTCAAGTTTGCTTAAATGAACCATAGAGCCAGTACTTTC

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	86.60%	1.80%	1.33%	10.26%	NA
All Indica	2759	97.90%	0.10%	0.11%	1.85%	NA
All Japonica	1512	62.80%	5.30%	3.97%	27.98%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	94.40%	0.00%	0.00%	5.59%	NA
Indica III	913	98.90%	0.00%	0.00%	1.10%	NA
Indica Intermediate	786	97.30%	0.40%	0.38%	1.91%	NA
Temperate Japonica	767	80.20%	1.60%	4.69%	13.56%	NA
Tropical Japonica	504	41.70%	3.40%	0.40%	54.56%	NA
Japonica Intermediate	241	51.50%	21.20%	9.13%	18.26%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	92.20%	1.10%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0403778987	C -> DEL	N	N	silent_mutation	Average:21.671; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0403778987	C -> T	LOC_Os04g07130.1	upstream_gene_variant ; 4294.0bp to feature; MODIFIER	silent_mutation	Average:21.671; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0403778987	C -> T	LOC_Os04g07120.1	downstream_gene_variant ; 1387.0bp to feature; MODIFIER	silent_mutation	Average:21.671; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0403778987	C -> T	LOC_Os04g07110-LOC_Os04g07120	intergenic_region ; MODIFIER	silent_mutation	Average:21.671; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0403778987	9.93E-07	1.04E-09	mr1698_2	Jap_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