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Detailed information for vg1200771325:

Variant ID: vg1200771325 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 771325
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

TGGACGCCGGGCTATACTTGAGTGATGCTGAGCAGAGGATTACCTTCGACCGGATGCAAGAGAAGATGCACGCTGTCATGCGCGTCTTCTCTTGTTGCAG[C/T]
GCCATGGACGCGGTACCTCCACCTGGTCCAGTACCACCATGTCCACGCGCCCCTAGTACCGGAGTTGTGCGACCTACAGCTGGTTCTTCGCACGGTACTG

Reverse complement sequence

CAGTACCGTGCGAAGAACCAGCTGTAGGTCGCACAACTCCGGTACTAGGGGCGCGTGGACATGGTGGTACTGGACCAGGTGGAGGTACCGCGTCCATGGC[G/A]
CTGCAACAAGAGAAGACGCGCATGACAGCGTGCATCTTCTCTTGCATCCGGTCGAAGGTAATCCTCTGCTCAGCATCACTCAAGTATAGCCCGGCGTCCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.50%	10.20%	0.30%	0.06%	NA
All Indica	2759	82.30%	17.10%	0.43%	0.11%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	85.50%	14.50%	0.00%	0.00%	NA
Indica II	465	94.60%	5.20%	0.22%	0.00%	NA
Indica III	913	71.00%	27.80%	0.88%	0.33%	NA
Indica Intermediate	786	85.80%	13.90%	0.38%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	4.40%	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
vg1200771325	C -> DEL	N	N	silent_mutation	Average:53.264; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N
vg1200771325	C -> T	LOC_Os12g02370.2	upstream_gene_variant ; 2768.0bp to feature; MODIFIER	silent_mutation	Average:53.264; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N
vg1200771325	C -> T	LOC_Os12g02370.4	upstream_gene_variant ; 2753.0bp to feature; MODIFIER	silent_mutation	Average:53.264; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N
vg1200771325	C -> T	LOC_Os12g02370-LOC_Os12g02380	intergenic_region ; MODIFIER	silent_mutation	Average:53.264; most accessible tissue: Minghui63 young leaf, score: 68.07	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200771325	3.21E-07	7.21E-06	mr1705	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