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Detailed information for vg1204397865:

Variant ID: vg1204397865 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4397865
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, G: 0.03, others allele: 0.00, population size: 32. )

Flanking Sequence (100 bp) in Reference Genome:

TAAAGGCTCGCAAGCTGCCGGACATGGATGCCAATGGCAGCCTTGATCCCTATGTCGAGGTCAAATTTGGTGCTTACAACAGGGGTGTCACCAGATGCTT[T/G]
AAGAGGAACAAGAACCCAGAGTGGAACGAGACTTTTGCTTTCTCCTTCCAGCATGACAAGATTCCCAGCCCCACTGTGGATATCGTAGTCAACGATAAGG

Reverse complement sequence

CCTTATCGTTGACTACGATATCCACAGTGGGGCTGGGAATCTTGTCATGCTGGAAGGAGAAAGCAAAAGTCTCGTTCCACTCTGGGTTCTTGTTCCTCTT[A/C]
AAGCATCTGGTGACACCCCTGTTGTAAGCACCAAATTTGACCTCGACATAGGGATCAAGGCTGCCATTGGCATCCATGTCCGGCAGCTTGCGAGCCTTTA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	33.40%	19.30%	1.16%	46.15%	NA
All Indica	2759	16.20%	4.00%	1.92%	77.93%	NA
All Japonica	1512	55.40%	43.80%	0.13%	0.66%	NA
Aus	269	59.10%	40.50%	0.00%	0.37%	NA
Indica I	595	10.30%	6.10%	2.18%	81.51%	NA
Indica II	465	23.00%	2.60%	1.94%	72.47%	NA
Indica III	913	14.00%	2.10%	1.86%	82.04%	NA
Indica Intermediate	786	19.20%	5.30%	1.78%	73.66%	NA
Temperate Japonica	767	27.90%	70.90%	0.26%	0.91%	NA
Tropical Japonica	504	83.90%	15.70%	0.00%	0.40%	NA
Japonica Intermediate	241	83.40%	16.20%	0.00%	0.41%	NA
VI/Aromatic	96	89.60%	8.30%	0.00%	2.08%	NA
Intermediate	90	52.20%	27.80%	0.00%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204397865	T -> DEL	LOC_Os12g08670.1	N	frameshift_variant	Average:11.747; most accessible tissue: Callus, score: 65.609	N	N	N	N
vg1204397865	T -> G	LOC_Os12g08670.1	missense_variant ; p.Phe238Leu; MODERATE	nonsynonymous_codon ; F238L	Average:11.747; most accessible tissue: Callus, score: 65.609	benign	-0.556	TOLERATED	0.23

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204397865	4.47E-06	NA	mr1111	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
vg1204397865	NA	1.92E-06	mr1543	Jap_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