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Detailed information for vg0410955533:

Variant ID: vg0410955533 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 10955533
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.58, T: 0.42, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

GACATTTACAAGGACAACAGAAATCTTTTGGCCTGACCTACCGACCCGTGGGCCCTGAAGGCCCACTCCTAGGCTGCTTATTGGGCTTCCTTGAGCAGGG[G/T]
TCACATGTCGCCGAACCGGCTTCGCCACTCAGTGGATCGGCTTCGCTTTCTACTGGCTGAGCTACGCCAACTGCGATCCGGCTTCATTATTCCGTGTTCT

Reverse complement sequence

AGAACACGGAATAATGAAGCCGGATCGCAGTTGGCGTAGCTCAGCCAGTAGAAAGCGAAGCCGATCCACTGAGTGGCGAAGCCGGTTCGGCGACATGTGA[C/A]
CCCTGCTCAAGGAAGCCCAATAAGCAGCCTAGGAGTGGGCCTTCAGGGCCCACGGGTCGGTAGGTCAGGCCAAAAGATTTCTGTTGTCCTTGTAAATGTC

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	64.90%	34.90%	0.02%	0.17%	NA
All Indica	2759	51.90%	47.70%	0.04%	0.29%	NA
All Japonica	1512	99.00%	1.00%	0.00%	0.00%	NA
Aus	269	0.00%	100.00%	0.00%	0.00%	NA
Indica I	595	77.00%	22.70%	0.00%	0.34%	NA
Indica II	465	48.60%	51.40%	0.00%	0.00%	NA
Indica III	913	41.70%	57.80%	0.11%	0.33%	NA
Indica Intermediate	786	46.80%	52.80%	0.00%	0.38%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	98.40%	1.60%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	85.40%	14.60%	0.00%	0.00%	NA
Intermediate	90	63.30%	36.70%	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
vg0410955533	G -> DEL	N	N	silent_mutation	Average:62.724; most accessible tissue: Zhenshan97 young leaf, score: 83.412	N	N	N	N
vg0410955533	G -> T	LOC_Os04g19640-LOC_Os04g19650	intergenic_region ; MODIFIER	silent_mutation	Average:62.724; most accessible tissue: Zhenshan97 young leaf, score: 83.412	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0410955533	NA	1.46E-14	mr1062	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
vg0410955533	NA	4.95E-06	mr1062	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
vg0410955533	NA	2.80E-13	mr1386	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
vg0410955533	NA	5.12E-06	mr1386	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
vg0410955533	NA	1.05E-09	mr1403	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
vg0410955533	NA	5.24E-08	mr1403	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
vg0410955533	NA	4.08E-07	mr1414	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
vg0410955533	NA	8.03E-09	mr1607	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
vg0410955533	NA	4.84E-06	mr1818	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
vg0410955533	NA	7.30E-18	mr1830	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
vg0410955533	NA	1.24E-09	mr1830	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
vg0410955533	6.81E-12	3.05E-30	mr1846	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
vg0410955533	3.60E-09	4.93E-17	mr1846	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
vg0410955533	NA	7.40E-06	mr1304_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
vg0410955533	NA	2.56E-06	mr1317_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
vg0410955533	NA	8.71E-08	mr1608_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
vg0410955533	NA	6.83E-06	mr1818_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
vg0410955533	NA	9.91E-18	mr1830_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
vg0410955533	NA	2.82E-14	mr1830_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
vg0410955533	6.28E-10	1.14E-47	mr1846_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
vg0410955533	1.03E-09	7.13E-30	mr1846_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