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Detailed information for vg0714477068:

Variant ID: vg0714477068 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14477068
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

GCAACTTCAACAGGCCGGTTGCAATTCAGAACCGCACTCCTACACCAACTATGGCTGCCCCTGAAGCCAAGAAGAATGTGGACTACTTCAACTGCGGGGA[G/A]
TACAGGCACTACGCCAACAACTGCCCTCATCCACGCAAAACTCCTGTCCGTACTGGCGCAAATGCAATGACTGTTCGTGGTACTGCTACCCCTGCTGCCG

Reverse complement sequence

CGGCAGCAGGGGTAGCAGTACCACGAACAGTCATTGCATTTGCGCCAGTACGGACAGGAGTTTTGCGTGGATGAGGGCAGTTGTTGGCGTAGTGCCTGTA[C/T]
TCCCCGCAGTTGAAGTAGTCCACATTCTTCTTGGCTTCAGGGGCAGCCATAGTTGGTGTAGGAGTGCGGTTCTGAATTGCAACCGGCCTGTTGAAGTTGC

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	61.80%	12.10%	10.45%	15.62%	NA
All Indica	2759	48.60%	18.40%	14.24%	18.77%	NA
All Japonica	1512	83.10%	3.40%	2.25%	11.24%	NA
Aus	269	66.50%	3.00%	14.13%	16.36%	NA
Indica I	595	41.80%	44.00%	12.77%	1.34%	NA
Indica II	465	63.90%	9.20%	11.61%	15.27%	NA
Indica III	913	39.10%	9.40%	15.88%	35.60%	NA
Indica Intermediate	786	55.70%	14.80%	15.01%	14.50%	NA
Temperate Japonica	767	82.10%	5.30%	0.78%	11.73%	NA
Tropical Japonica	504	94.00%	2.00%	0.60%	3.37%	NA
Japonica Intermediate	241	63.10%	0.40%	10.37%	26.14%	NA
VI/Aromatic	96	80.20%	0.00%	19.79%	0.00%	NA
Intermediate	90	77.80%	4.40%	11.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714477068	G -> DEL	LOC_Os07g25340.1	N	frameshift_variant	Average:20.723; most accessible tissue: Callus, score: 61.803	N	N	N	N
vg0714477068	G -> A	LOC_Os07g25340.1	synonymous_variant ; p.Glu354Glu; LOW	synonymous_codon	Average:20.723; most accessible tissue: Callus, score: 61.803	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714477068	NA	3.40E-14	mr1026	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
vg0714477068	NA	1.14E-16	mr1118	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
vg0714477068	NA	1.09E-13	mr1161	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
vg0714477068	NA	8.83E-07	mr1242	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
vg0714477068	NA	2.76E-19	mr1495	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
vg0714477068	NA	1.24E-08	mr1496	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
vg0714477068	NA	5.52E-09	mr1794	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
vg0714477068	NA	2.41E-06	mr1936	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
vg0714477068	NA	3.08E-17	mr1118_2	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
vg0714477068	NA	8.50E-23	mr1118_2	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
vg0714477068	NA	2.46E-08	mr1123_2	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
vg0714477068	NA	2.06E-10	mr1161_2	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
vg0714477068	NA	7.01E-08	mr1242_2	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
vg0714477068	NA	9.99E-23	mr1495_2	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
vg0714477068	NA	3.47E-22	mr1495_2	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
vg0714477068	NA	1.77E-10	mr1496_2	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
vg0714477068	NA	1.77E-13	mr1794_2	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
vg0714477068	NA	4.68E-09	mr1936_2	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