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Detailed information for vg0400771373:

Variant ID: vg0400771373 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 771373
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

ATGATAGGCTAGGATACAGAGGATTTACTAGTGAGAAACAGTGTCTAGGGAAAGCTTAATTTTAATCCTAATGCAATACTTCAGGCACTGGCAACCTGCT[A/C]
TTCCCAGATGTCGCTCTACTACGTACCCGGACAAGGAGGACTTAAGTGATCTTGAGGGCTGTCACCACCTCTACACCTACCTCAACGTACTGTGGGATAC

Reverse complement sequence

GTATCCCACAGTACGTTGAGGTAGGTGTAGAGGTGGTGACAGCCCTCAAGATCACTTAAGTCCTCCTTGTCCGGGTACGTAGTAGAGCGACATCTGGGAA[T/G]
AGCAGGTTGCCAGTGCCTGAAGTATTGCATTAGGATTAAAATTAAGCTTTCCCTAGACACTGTTTCTCACTAGTAAATCCTCTGTATCCTAGCCTATCAT

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	60.20%	3.80%	0.70%	35.32%	NA
All Indica	2759	35.60%	6.50%	1.12%	56.80%	NA
All Japonica	1512	96.40%	0.00%	0.00%	3.57%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	16.50%	2.20%	2.35%	78.99%	NA
Indica II	465	41.30%	5.20%	1.08%	52.47%	NA
Indica III	913	42.90%	10.60%	0.55%	45.89%	NA
Indica Intermediate	786	38.20%	5.70%	0.89%	55.22%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	90.70%	0.00%	0.00%	9.33%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	72.90%	0.00%	0.00%	27.08%	NA
Intermediate	90	73.30%	1.10%	2.22%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0400771373	A -> C	LOC_Os04g02230.1	upstream_gene_variant ; 620.0bp to feature; MODIFIER	silent_mutation	Average:30.203; most accessible tissue: Minghui63 flag leaf, score: 79.383	N	N	N	N
vg0400771373	A -> C	LOC_Os04g02240.1	upstream_gene_variant ; 3406.0bp to feature; MODIFIER	silent_mutation	Average:30.203; most accessible tissue: Minghui63 flag leaf, score: 79.383	N	N	N	N
vg0400771373	A -> C	LOC_Os04g02230-LOC_Os04g02240	intergenic_region ; MODIFIER	silent_mutation	Average:30.203; most accessible tissue: Minghui63 flag leaf, score: 79.383	N	N	N	N
vg0400771373	A -> DEL	N	N	silent_mutation	Average:30.203; most accessible tissue: Minghui63 flag leaf, score: 79.383	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400771373	NA	2.32E-06	mr1057	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
vg0400771373	6.29E-07	6.29E-07	mr1551	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