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Detailed information for vg0617262301:

Variant ID: vg0617262301 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 17262301
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: 123. )

Flanking Sequence (100 bp) in Reference Genome:

ATATAGAGCAAATATAGTTAAATCAGATAAGATCGGCTGAAACTCCGATGCTACCCTAATCGGCAACCAGAAGACAGGCTAGAGGTTGATATTCTAAGCA[C/T]
GACTTAATAGATCAAACTTAACTGATGCAGCATTAAGTATAAAAAGAAGAACAATATCTAGACAATCAAACCACTGGAAGTTTCATAAAGTGGTAAATAT

Reverse complement sequence

ATATTTACCACTTTATGAAACTTCCAGTGGTTTGATTGTCTAGATATTGTTCTTCTTTTTATACTTAATGCTGCATCAGTTAAGTTTGATCTATTAAGTC[G/A]
TGCTTAGAATATCAACCTCTAGCCTGTCTTCTGGTTGCCGATTAGGGTAGCATCGGAGTTTCAGCCGATCTTATCTGATTTAACTATATTTGCTCTATAT

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	62.40%	0.10%	6.92%	30.53%	NA
All Indica	2759	45.80%	0.10%	5.26%	48.79%	NA
All Japonica	1512	97.50%	0.00%	0.33%	2.18%	NA
Aus	269	50.60%	0.70%	35.32%	13.38%	NA
Indica I	595	31.10%	0.20%	4.54%	64.20%	NA
Indica II	465	20.60%	0.00%	3.44%	75.91%	NA
Indica III	913	72.70%	0.10%	5.70%	21.47%	NA
Indica Intermediate	786	40.70%	0.10%	6.36%	52.80%	NA
Temperate Japonica	767	96.20%	0.00%	0.13%	3.65%	NA
Tropical Japonica	504	99.40%	0.00%	0.20%	0.40%	NA
Japonica Intermediate	241	97.50%	0.00%	1.24%	1.24%	NA
VI/Aromatic	96	15.60%	0.00%	72.92%	11.46%	NA
Intermediate	90	67.80%	0.00%	13.33%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0617262301	C -> T	LOC_Os06g29994.1	intron_variant ; MODIFIER	silent_mutation	Average:17.801; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0617262301	C -> DEL	N	N	silent_mutation	Average:17.801; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0617262301	NA	2.12E-06	mr1254	Ind_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
vg0617262301	2.81E-06	5.81E-07	mr1804	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