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Detailed information for vg0320738098:

Variant ID: vg0320738098 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 20738098
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:

GGTGCTCGAGCCCCTGCCGTTGTCACTCATTGCCAGCCACCAGCTCCCGCATCTTCTGGAGGTCCTCGCGAACCTCCGCTAAGTCGCGCGCCAGCCGGTC[G/A]
GCGCGCTTTTCGCCGACGACGCTGCCGCCGCCCTTGCCTCCGCAATCTCGCGACCAATGCCGCGAGCACCAGCCTTGGGGAGGCGCCCCATCTCGACCTG

Reverse complement sequence

CAGGTCGAGATGGGGCGCCTCCCCAAGGCTGGTGCTCGCGGCATTGGTCGCGAGATTGCGGAGGCAAGGGCGGCGGCAGCGTCGTCGGCGAAAAGCGCGC[C/T]
GACCGGCTGGCGCGCGACTTAGCGGAGGTTCGCGAGGACCTCCAGAAGATGCGGGAGCTGGTGGCTGGCAATGAGTGACAACGGCAGGGGCTCGAGCACC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.40%	9.50%	10.18%	37.92%	NA
All Indica	2759	10.40%	14.70%	14.97%	59.99%	NA
All Japonica	1512	96.50%	0.90%	2.05%	0.53%	NA
Aus	269	43.50%	10.80%	5.58%	40.15%	NA
Indica I	595	3.70%	2.90%	4.54%	88.91%	NA
Indica II	465	26.70%	9.20%	23.87%	40.22%	NA
Indica III	913	5.80%	24.10%	16.32%	53.78%	NA
Indica Intermediate	786	11.10%	15.90%	16.03%	57.00%	NA
Temperate Japonica	767	99.70%	0.00%	0.13%	0.13%	NA
Tropical Japonica	504	91.90%	2.60%	4.76%	0.79%	NA
Japonica Intermediate	241	95.90%	0.40%	2.49%	1.24%	NA
VI/Aromatic	96	85.40%	0.00%	13.54%	1.04%	NA
Intermediate	90	64.40%	3.30%	10.00%	22.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0320738098	G -> A	LOC_Os03g37411.1	intron_variant ; MODIFIER	silent_mutation	Average:22.633; most accessible tissue: Minghui63 young leaf, score: 50.756	N	N	N	N
vg0320738098	G -> DEL	N	N	silent_mutation	Average:22.633; most accessible tissue: Minghui63 young leaf, score: 50.756	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0320738098	2.62E-06	2.62E-06	mr1540	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
vg0320738098	NA	5.39E-06	mr1662	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
vg0320738098	NA	8.12E-07	mr1732	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
vg0320738098	NA	5.89E-06	mr1133_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