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Detailed information for vg0514066405:

Variant ID: vg0514066405 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14066405
Reference Allele: G	Alternative Allele: A,C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCAAAGGCCAGCAGGTTTTCTACAACCTCTTCAGATCCCGAAATGGAAATGGGAGGAGATTGGAATGGACTTCATAACAGGACTGCCCCGGACATCATCT[G/A,C]
GCCACGATTCAATCTGGGTAGTCGTGAATCGACTCACTAAAGTTGCCCATTTCATTCCAGTGCATACCACGTATACGGGGAAGAAATTGGCAGAGCTGTA

Reverse complement sequence

TACAGCTCTGCCAATTTCTTCCCCGTATACGTGGTATGCACTGGAATGAAATGGGCAACTTTAGTGAGTCGATTCACGACTACCCAGATTGAATCGTGGC[C/T,G]
AGATGATGTCCGGGGCAGTCCTGTTATGAAGTCCATTCCAATCTCCTCCCATTTCCATTTCGGGATCTGAAGAGGTTGTAGAAAACCTGCTGGCCTTTGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	73.30%	5.60%	13.92%	7.15%	A: 0.02%
All Indica	2759	55.10%	9.50%	23.60%	11.82%	NA
All Japonica	1512	99.90%	0.00%	0.00%	0.07%	NA
Aus	269	97.00%	0.40%	1.49%	1.12%	NA
Indica I	595	78.70%	2.90%	13.28%	5.21%	NA
Indica II	465	38.30%	14.80%	30.11%	16.77%	NA
Indica III	913	48.80%	11.40%	26.07%	13.69%	NA
Indica Intermediate	786	54.50%	9.20%	24.68%	11.70%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	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	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	0.00%	3.33%	8.89%	A: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0514066405	G -> DEL	LOC_Os05g24310.1	N	frameshift_variant	Average:44.801; most accessible tissue: Zhenshan97 flag leaf, score: 74.498	N	N	N	N
vg0514066405	G -> C	LOC_Os05g24310.1	missense_variant ; p.Gly833Arg; MODERATE	nonsynonymous_codon ; G833R	Average:44.801; most accessible tissue: Zhenshan97 flag leaf, score: 74.498	unknown	unknown	DELETERIOUS	0.01
vg0514066405	G -> A	LOC_Os05g24310.1	missense_variant ; p.Gly833Ser; MODERATE	nonsynonymous_codon ; G833S	Average:44.801; most accessible tissue: Zhenshan97 flag leaf, score: 74.498	unknown	unknown	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514066405	4.64E-08	NA	mr1632	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
vg0514066405	3.03E-06	9.11E-06	mr1632	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