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Detailed information for vg1114670020:

Variant ID: vg1114670020 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 14670020
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 350. )

Flanking Sequence (100 bp) in Reference Genome:

GATGACAAGTCTTCCCATAGACAAGTTGGTATGGTGACATGCCGATGGGCGTCTTATAAGCAGTCCTATATGCCCAAAGTGCATCAGATAGCTTGTTCTT[C/T]
CATGCCTTCCCCATCTCATTGACAGTCTTCTGTAGAATATTCTTGATTTGTTTGTTACTCGTTTCTGCCTGTCCACTTGTCTGGGGATGATATGGAGTGG

Reverse complement sequence

CCACTCCATATCATCCCCAGACAAGTGGACAGGCAGAAACGAGTAACAAACAAATCAAGAATATTCTACAGAAGACTGTCAATGAGATGGGGAAGGCATG[G/A]
AAGAACAAGCTATCTGATGCACTTTGGGCATATAGGACTGCTTATAAGACGCCCATCGGCATGTCACCATACCAACTTGTCTATGGGAAGACTTGTCATC

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	94.10%	4.80%	1.08%	0.00%	NA
All Indica	2759	99.60%	0.40%	0.00%	0.00%	NA
All Japonica	1512	82.50%	14.10%	3.37%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.50%	0.00%	0.00%	NA
Temperate Japonica	767	73.30%	21.40%	5.35%	0.00%	NA
Tropical Japonica	504	96.80%	1.80%	1.39%	0.00%	NA
Japonica Intermediate	241	82.20%	16.60%	1.24%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	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
vg1114670020	C -> T	LOC_Os11g25720.1	intron_variant ; MODIFIER	silent_mutation	Average:50.224; most accessible tissue: Minghui63 young leaf, score: 72.959	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1114670020	NA	3.92E-07	mr1424	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
vg1114670020	4.40E-06	4.40E-06	mr1464	Jap_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