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Detailed information for vg1200191651:

Variant ID: vg1200191651 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 191651
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.73, G: 0.27, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTTTTCTGTGACTTGGTTTTCTTCTTTGGAGCCTGAGCCGATGGGTCTACTGCCAATGACCTGGTTTTCCTCTTTTTTCCGGCATCGGCTGATTCTCT[T/G]
ATGAGCCCTTGAAGAAGAGTTGAAGTCTTGGGGGCATTATAGCCGATGACAGGAGGAGATGGTCCACCTCCATTAGGAATGAGACCCGGAGCATATTCAA

Reverse complement sequence

TTGAATATGCTCCGGGTCTCATTCCTAATGGAGGTGGACCATCTCCTCCTGTCATCGGCTATAATGCCCCCAAGACTTCAACTCTTCTTCAAGGGCTCAT[A/C]
AGAGAATCAGCCGATGCCGGAAAAAAGAGGAAAACCAGGTCATTGGCAGTAGACCCATCGGCTCAGGCTCCAAAGAAGAAAACCAAGTCACAGAAAACTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.00%	11.30%	0.68%	41.01%	NA
All Indica	2759	17.80%	13.70%	1.09%	67.42%	NA
All Japonica	1512	96.10%	0.30%	0.07%	3.57%	NA
Aus	269	48.70%	50.60%	0.00%	0.74%	NA
Indica I	595	18.80%	23.20%	1.34%	56.64%	NA
Indica II	465	12.70%	0.60%	0.65%	86.02%	NA
Indica III	913	18.30%	12.30%	0.66%	68.78%	NA
Indica Intermediate	786	19.50%	15.90%	1.65%	62.98%	NA
Temperate Japonica	767	94.70%	0.00%	0.13%	5.22%	NA
Tropical Japonica	504	97.40%	0.40%	0.00%	2.18%	NA
Japonica Intermediate	241	97.90%	0.80%	0.00%	1.24%	NA
VI/Aromatic	96	92.70%	5.20%	0.00%	2.08%	NA
Intermediate	90	63.30%	13.30%	1.11%	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
vg1200191651	T -> DEL	LOC_Os12g01340.1	N	frameshift_variant	Average:8.335; most accessible tissue: Callus, score: 27.146	N	N	N	N
vg1200191651	T -> G	LOC_Os12g01340.1	synonymous_variant ; p.Ile368Ile; LOW	synonymous_codon	Average:8.335; most accessible tissue: Callus, score: 27.146	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200191651	6.75E-06	NA	mr1489	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
vg1200191651	NA	3.69E-06	mr1274_2	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