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Detailed information for vg0617762306:

Variant ID: vg0617762306 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 17762306
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, C: 0.08, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

CTAGAAGACCATTCAATCAATGATGTACCAAGAAAATGACATGTTCCACTAGTACTTTTCCTATCAATTTTACAACCTCCAAAATCAGCATCGGAATATC[T/C]
ACTTAAGCATATAGAAGATGAAGTAGAATACCAAATTCCAAACTCAAGTGTATGATTCAAATACCTCATTATTCGGTTGACCGCTTGACGATGTGAAGCA

Reverse complement sequence

TGCTTCACATCGTCAAGCGGTCAACCGAATAATGAGGTATTTGAATCATACACTTGAGTTTGGAATTTGGTATTCTACTTCATCTTCTATATGCTTAAGT[A/G]
GATATTCCGATGCTGATTTTGGAGGTTGTAAAATTGATAGGAAAAGTACTAGTGGAACATGTCATTTTCTTGGTACATCATTGATTGAATGGTCTTCTAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.70%	1.90%	3.94%	1.46%	NA
All Indica	2759	99.20%	0.20%	0.43%	0.14%	NA
All Japonica	1512	82.40%	4.40%	8.99%	4.23%	NA
Aus	269	82.50%	4.50%	13.01%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	98.10%	0.40%	0.86%	0.65%	NA
Indica III	913	99.50%	0.00%	0.44%	0.11%	NA
Indica Intermediate	786	99.00%	0.50%	0.51%	0.00%	NA
Temperate Japonica	767	99.00%	0.00%	0.39%	0.65%	NA
Tropical Japonica	504	57.10%	11.90%	21.23%	9.72%	NA
Japonica Intermediate	241	82.60%	2.50%	10.79%	4.15%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	92.20%	4.40%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0617762306	T -> C	LOC_Os06g30670.1	intron_variant ; MODIFIER	silent_mutation	Average:19.909; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg0617762306	T -> DEL	N	N	silent_mutation	Average:19.909; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0617762306	2.33E-08	NA	mr1745_2	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