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Detailed information for vg0603243535:

Variant ID: vg0603243535 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 3243535
Reference Allele: G	Alternative Allele: T,C
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

AAAGGTACAGGACCAGACGGATCCAACAAGGTCATAAAGTTCTCCTCTACTGATTTGGACACTATGAAATTAAGAATGACGTCGTGAACACGGCAGCTCA[G/T,C]
CACCTCACCGTAGTGCTCATTCCATGGTTGGATCAAGCTCTGGTTTATCAGCACATTGAAATACCTCAGCCCTGCTTCATATAGATTTTCTCCTGGTCTT

Reverse complement sequence

AAGACCAGGAGAAAATCTATATGAAGCAGGGCTGAGGTATTTCAATGTGCTGATAAACCAGAGCTTGATCCAACCATGGAATGAGCACTACGGTGAGGTG[C/A,G]
TGAGCTGCCGTGTTCACGACGTCATTCTTAATTTCATAGTGTCCAAATCAGTAGAGGAGAACTTTATGACCTTGTTGGATCCGTCTGGTCCTGTACCTTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	81.90%	16.20%	0.13%	0.34%	C: 1.40%
All Indica	2759	77.10%	20.10%	0.18%	0.25%	C: 2.39%
All Japonica	1512	97.30%	2.10%	0.00%	0.60%	NA
Aus	269	68.40%	31.20%	0.37%	0.00%	NA
Indica I	595	83.90%	15.10%	0.17%	0.50%	C: 0.34%
Indica II	465	88.80%	9.90%	0.00%	0.00%	C: 1.29%
Indica III	913	67.90%	27.10%	0.33%	0.22%	C: 4.49%
Indica Intermediate	786	75.60%	21.90%	0.13%	0.25%	C: 2.16%
Temperate Japonica	767	95.80%	3.00%	0.00%	1.17%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.10%	2.90%	0.00%	0.00%	NA
VI/Aromatic	96	16.70%	83.30%	0.00%	0.00%	NA
Intermediate	90	82.20%	17.80%	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
vg0603243535	G -> C	LOC_Os06g06860.1	missense_variant ; p.Leu295Val; MODERATE	nonsynonymous_codon ; L295V	Average:64.191; most accessible tissue: Callus, score: 82.707	benign	0.075	TOLERATED	0.52
vg0603243535	G -> T	LOC_Os06g06860.1	missense_variant ; p.Leu295Met; MODERATE	nonsynonymous_codon ; L295M	Average:64.191; most accessible tissue: Callus, score: 82.707	benign	0.47	TOLERATED	0.29
vg0603243535	G -> DEL	LOC_Os06g06860.1	N	frameshift_variant	Average:64.191; most accessible tissue: Callus, score: 82.707	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0603243535	1.84E-07	8.68E-12	Heading_date	All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0603243535	NA	8.92E-07	mr1705	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