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Detailed information for vg1003424866:

Variant ID: vg1003424866 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3424866
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, C: 0.22, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TACACTTATCTCCAAGGCACTATAAGGTAACACCAAAAGGCCATCTCTTCTAAAAGCACAATTCATATTAAGAATTTGAAATAACAATGGACCTTAAAAT[G/C]
GCTATTTATAGTTAACACACATGTGTGCTGGTGCACGCACACTGTTATGTGGGGGACCACGTATAGCAAGCACAGGAAACCAGGTGCACTGGACACACCG

Reverse complement sequence

CGGTGTGTCCAGTGCACCTGGTTTCCTGTGCTTGCTATACGTGGTCCCCCACATAACAGTGTGCGTGCACCAGCACACATGTGTGTTAACTATAAATAGC[C/G]
ATTTTAAGGTCCATTGTTATTTCAAATTCTTAATATGAATTGTGCTTTTAGAAGAGATGGCCTTTTGGTGTTACCTTATAGTGCCTTGGAGATAAGTGTA

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	59.40%	40.10%	0.21%	0.21%	NA
All Indica	2759	43.50%	55.90%	0.29%	0.36%	NA
All Japonica	1512	98.30%	1.70%	0.07%	0.00%	NA
Aus	269	7.10%	92.90%	0.00%	0.00%	NA
Indica I	595	46.70%	52.80%	0.34%	0.17%	NA
Indica II	465	25.60%	73.30%	0.43%	0.65%	NA
Indica III	913	58.80%	40.40%	0.33%	0.44%	NA
Indica Intermediate	786	33.70%	65.90%	0.13%	0.25%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	96.20%	3.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.41%	0.00%	NA
VI/Aromatic	96	58.30%	41.70%	0.00%	0.00%	NA
Intermediate	90	54.40%	44.40%	1.11%	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
vg1003424866	G -> C	LOC_Os10g06610.1	intron_variant ; MODIFIER	silent_mutation	Average:55.444; most accessible tissue: Zhenshan97 young leaf, score: 69.263	N	N	N	N
vg1003424866	G -> DEL	N	N	silent_mutation	Average:55.444; most accessible tissue: Zhenshan97 young leaf, score: 69.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003424866	NA	1.10E-06	mr1291	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
vg1003424866	4.21E-12	NA	mr1538	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
vg1003424866	2.37E-12	3.69E-14	mr1538	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
vg1003424866	1.83E-19	2.57E-13	mr1547	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
vg1003424866	1.93E-18	7.09E-25	mr1547	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
vg1003424866	1.51E-36	1.81E-46	mr1709	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
vg1003424866	6.85E-42	2.61E-66	mr1709	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
vg1003424866	NA	8.78E-07	mr1129_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
vg1003424866	3.54E-11	NA	mr1538_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
vg1003424866	4.44E-15	1.82E-20	mr1538_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
vg1003424866	7.45E-21	1.72E-19	mr1547_2	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
vg1003424866	2.74E-23	1.16E-31	mr1547_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
vg1003424866	2.84E-61	8.11E-74	mr1709_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
vg1003424866	7.73E-61	4.09E-108	mr1709_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