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Detailed information for vg0405622759:

Variant ID: vg0405622759 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5622759
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

GAACTTGGGTTGCCACACTGGTTTCTCGCCCTTATCCAGAAATACCAGGATGGGGTGGTTATTTGTTCCTTATAAATAATGGTTTTTGTGGTGATGCATG[G/C]
CAGCTACTACGTAAACTGTTTGCCCCCCAGAGGGTGCAAAACTGCAAATAACTGTGCCACTGCTATAATCTTAAGCAACATTTTGCCAAAATAACTACTG

Reverse complement sequence

CAGTAGTTATTTTGGCAAAATGTTGCTTAAGATTATAGCAGTGGCACAGTTATTTGCAGTTTTGCACCCTCTGGGGGGCAAACAGTTTACGTAGTAGCTG[C/G]
CATGCATCACCACAAAAACCATTATTTATAAGGAACAAATAACCACCCCATCCTGGTATTTCTGGATAAGGGCGAGAAACCAGTGTGGCAACCCAAGTTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.10%	4.60%	3.28%	0.00%	NA
All Indica	2759	99.00%	0.30%	0.69%	0.00%	NA
All Japonica	1512	77.90%	13.40%	8.66%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.20%	0.20%	0.67%	0.00%	NA
Indica II	465	98.70%	0.90%	0.43%	0.00%	NA
Indica III	913	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	98.00%	0.50%	1.53%	0.00%	NA
Temperate Japonica	767	64.80%	23.30%	11.86%	0.00%	NA
Tropical Japonica	504	96.80%	1.20%	1.98%	0.00%	NA
Japonica Intermediate	241	80.10%	7.50%	12.45%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	7.80%	5.56%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405622759	G -> C	LOC_Os04g10380.1	intron_variant ; MODIFIER	silent_mutation	Average:61.134; most accessible tissue: Callus, score: 80.223	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405622759	4.83E-06	NA	mr1631	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
vg0405622759	NA	7.36E-07	mr1977	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