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Detailed information for vg0114394801:

Variant ID: vg0114394801 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14394801
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, C: 0.01, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

TCATGTTTACAACTCAGAGAAACAGAGCAGAAAATATGCAAGGCGCCCGGGACCCTGGGCAGGGGGTGGGGGGGGGGTTGGGGGGTGGACATGTTTGCTC[G/C]
AGTATTCTGCATGTTGGTCATGTATATTATACCTAACTTAGTTTTGACTTACTGAGATAATGTGACATAATTCTGATTAAAATCAACTGGTTCGTAATAA

Reverse complement sequence

TTATTACGAACCAGTTGATTTTAATCAGAATTATGTCACATTATCTCAGTAAGTCAAAACTAAGTTAGGTATAATATACATGACCAACATGCAGAATACT[C/G]
GAGCAAACATGTCCACCCCCCAACCCCCCCCCCACCCCCTGCCCAGGGTCCCGGGCGCCTTGCATATTTTCTGCTCTGTTTCTCTGAGTTGTAAACATGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.10%	18.80%	0.11%	0.00%	NA
All Indica	2759	72.90%	27.00%	0.14%	0.00%	NA
All Japonica	1512	97.50%	2.50%	0.00%	0.00%	NA
Aus	269	70.30%	29.40%	0.37%	0.00%	NA
Indica I	595	63.70%	36.10%	0.17%	0.00%	NA
Indica II	465	90.50%	9.50%	0.00%	0.00%	NA
Indica III	913	67.30%	32.60%	0.11%	0.00%	NA
Indica Intermediate	786	76.00%	23.80%	0.25%	0.00%	NA
Temperate Japonica	767	98.70%	1.30%	0.00%	0.00%	NA
Tropical Japonica	504	95.00%	5.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	0.00%	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
vg0114394801	G -> C	LOC_Os01g25440.1	intron_variant ; MODIFIER	silent_mutation	Average:61.674; most accessible tissue: Callus, score: 82.069	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114394801	NA	5.01E-06	mr1064	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
vg0114394801	3.77E-08	NA	mr1519_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
vg0114394801	7.15E-08	2.39E-11	mr1519_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