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Detailed information for vg0137432669:

Variant ID: vg0137432669 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 37432669
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

CAGGCTGGCGGTTCGGTTTCGGATTGCGCCACCGCGTACGGCGATTGCTGTGCGCGCGTATCGGCGGCCTTCACCTTGGGCCTTTTGCAACAGTTCGGTT[G/A]
CGAGCACGTCGCCGAGTTCCCTAACTATGCGAAGGGGGACTGGGAGATTAGTGCGCAGAATATTTCGCCCGCTCTTCGTGCATGGCGAAAACAGTTCTGG

Reverse complement sequence

CCAGAACTGTTTTCGCCATGCACGAAGAGCGGGCGAAATATTCTGCGCACTAATCTCCCAGTCCCCCTTCGCATAGTTAGGGAACTCGGCGACGTGCTCG[C/T]
AACCGAACTGTTGCAAAAGGCCCAAGGTGAAGGCCGCCGATACGCGCGCACAGCAATCGCCGTACGCGGTGGCGCAATCCGAAACCGAACCGCCAGCCTG

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	91.90%	5.10%	3.03%	0.00%	NA
All Indica	2759	86.50%	8.50%	4.97%	0.00%	NA
All Japonica	1512	99.70%	0.10%	0.13%	0.00%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	60.20%	23.20%	16.64%	0.00%	NA
Indica II	465	95.70%	2.60%	1.72%	0.00%	NA
Indica III	913	96.90%	2.80%	0.22%	0.00%	NA
Indica Intermediate	786	88.90%	7.50%	3.56%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	2.22%	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
vg0137432669	G -> A	LOC_Os01g64510.1	3_prime_UTR_variant ; 337.0bp to feature; MODIFIER	silent_mutation	Average:50.563; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0137432669	1.07E-06	7.89E-07	mr1517	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