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Detailed information for vg0706489091:

Variant ID: vg0706489091 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6489091
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATACTCACCCTTATAAACACACACACGCACATCCTACCCCTATGAGTATCTTCTAAAGACTGGGCCGATATATTTTTGAGATTGACGAAATCACCACGA[G/A,T]
CGCCTCGCTACCAATGGGTATGTCAACACTGAAATAATAGTTAACCATAAATGCGAGCACCCATGTCAAATCTAGGACTTAAATCCGGGCAGGCATGTTC

Reverse complement sequence

GAACATGCCTGCCCGGATTTAAGTCCTAGATTTGACATGGGTGCTCGCATTTATGGTTAACTATTATTTCAGTGTTGACATACCCATTGGTAGCGAGGCG[C/T,A]
TCGTGGTGATTTCGTCAATCTCAAAAATATATCGGCCCAGTCTTTAGAAGATACTCATAGGGGTAGGATGTGCGTGTGTGTGTTTATAAGGGTGAGTATG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.50%	4.20%	7.26%	8.25%	T: 2.75%
All Indica	2759	74.40%	6.30%	9.50%	8.95%	T: 0.80%
All Japonica	1512	91.10%	0.00%	1.39%	0.53%	T: 7.01%
Aus	269	25.30%	7.10%	19.70%	47.58%	T: 0.37%
Indica I	595	73.60%	3.50%	13.28%	7.23%	T: 2.35%
Indica II	465	90.30%	1.30%	5.38%	2.37%	T: 0.65%
Indica III	913	69.40%	10.40%	7.78%	12.27%	T: 0.11%
Indica Intermediate	786	71.50%	6.60%	11.07%	10.31%	T: 0.51%
Temperate Japonica	767	84.10%	0.00%	2.74%	0.00%	T: 13.17%
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	95.90%	0.00%	0.00%	2.07%	T: 2.07%
VI/Aromatic	96	92.70%	3.10%	1.04%	3.12%	NA
Intermediate	90	84.40%	3.30%	6.67%	4.44%	T: 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
vg0706489091	G -> DEL	N	N	silent_mutation	Average:46.011; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg0706489091	G -> A	LOC_Os07g11720-LOC_Os07g11739	intergenic_region ; MODIFIER	silent_mutation	Average:46.011; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg0706489091	G -> T	LOC_Os07g11720-LOC_Os07g11739	intergenic_region ; MODIFIER	silent_mutation	Average:46.011; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706489091	3.60E-06	3.60E-06	mr1803	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