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Detailed information for vg0610620315:

Variant ID: vg0610620315 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10620315
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

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

Flanking Sequence (100 bp) in Reference Genome:

CAAGGATGCAGTCACTAGGACAATGCCAGCTATATCTCCCCCGAATCAAAGTGAGCAGCCCCGTTTGTGGTTTTCAGTTCGCTACTTATCATTGTGTAAT[A/C]
GAAAGTTTGTAGCAATCATGTAATAAATAAATATATTCATGATTATAAACAATGAGTTCGTTATGTTTATGGAAGATTCATGTTGAGGATGCAATGTACC

Reverse complement sequence

GGTACATTGCATCCTCAACATGAATCTTCCATAAACATAACGAACTCATTGTTTATAATCATGAATATATTTATTTATTACATGATTGCTACAAACTTTC[T/G]
ATTACACAATGATAAGTAGCGAACTGAAAACCACAAACGGGGCTGCTCACTTTGATTCGGGGGAGATATAGCTGGCATTGTCCTAGTGACTGCATCCTTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.80%	2.90%	3.20%	23.09%	NA
All Indica	2759	65.90%	1.50%	3.12%	29.50%	NA
All Japonica	1512	79.90%	6.00%	3.31%	10.85%	NA
Aus	269	59.10%	0.40%	3.72%	36.80%	NA
Indica I	595	41.80%	0.00%	2.18%	55.97%	NA
Indica II	465	54.00%	7.10%	3.01%	35.91%	NA
Indica III	913	88.70%	0.00%	2.63%	8.65%	NA
Indica Intermediate	786	64.60%	1.00%	4.45%	29.90%	NA
Temperate Japonica	767	79.00%	0.10%	1.83%	19.04%	NA
Tropical Japonica	504	77.40%	15.70%	5.95%	0.99%	NA
Japonica Intermediate	241	88.00%	4.10%	2.49%	5.39%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	71.10%	7.80%	5.56%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0610620315	A -> C	LOC_Os06g18730.1	downstream_gene_variant ; 140.0bp to feature; MODIFIER	silent_mutation	Average:29.321; most accessible tissue: Minghui63 young leaf, score: 48.378	N	N	N	N
vg0610620315	A -> C	LOC_Os06g18730-LOC_Os06g18740	intergenic_region ; MODIFIER	silent_mutation	Average:29.321; most accessible tissue: Minghui63 young leaf, score: 48.378	N	N	N	N
vg0610620315	A -> DEL	N	N	silent_mutation	Average:29.321; most accessible tissue: Minghui63 young leaf, score: 48.378	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610620315	8.91E-11	NA	mr1016	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
vg0610620315	8.27E-08	NA	mr1017	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
vg0610620315	3.50E-10	NA	mr1018	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
vg0610620315	4.78E-06	NA	mr1019	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
vg0610620315	2.48E-08	NA	mr1022	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
vg0610620315	2.90E-10	NA	mr1023	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
vg0610620315	3.21E-10	NA	mr1055	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
vg0610620315	3.95E-12	NA	mr1079	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
vg0610620315	3.32E-06	NA	mr1079	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
vg0610620315	9.02E-11	NA	mr1132	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
vg0610620315	2.07E-11	NA	mr1142	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
vg0610620315	8.52E-10	NA	mr1178	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
vg0610620315	1.19E-08	NA	mr1390	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
vg0610620315	1.34E-12	NA	mr1489	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
vg0610620315	1.56E-06	NA	mr1489	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
vg0610620315	1.25E-08	NA	mr1490	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
vg0610620315	1.91E-11	NA	mr1491	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
vg0610620315	4.92E-06	NA	mr1491	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
vg0610620315	4.66E-08	NA	mr1778	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
vg0610620315	4.66E-07	NA	mr1019_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
vg0610620315	2.41E-10	NA	mr1022_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
vg0610620315	4.06E-06	NA	mr1022_2	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
vg0610620315	3.86E-11	NA	mr1023_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
vg0610620315	2.86E-06	NA	mr1023_2	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
vg0610620315	1.38E-10	NA	mr1055_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
vg0610620315	1.60E-06	NA	mr1055_2	Jap_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
vg0610620315	3.36E-11	NA	mr1079_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
vg0610620315	5.58E-07	NA	mr1079_2	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
vg0610620315	1.89E-10	NA	mr1132_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
vg0610620315	8.71E-06	NA	mr1132_2	Jap_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
vg0610620315	1.09E-11	NA	mr1178_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
vg0610620315	7.72E-06	NA	mr1261_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
vg0610620315	1.24E-09	NA	mr1390_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
vg0610620315	1.04E-06	NA	mr1390_2	Jap_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
vg0610620315	1.15E-12	NA	mr1489_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
vg0610620315	1.33E-09	NA	mr1490_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
vg0610620315	1.32E-06	NA	mr1490_2	Jap_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
vg0610620315	2.08E-06	NA	mr1778_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
vg0610620315	NA	6.33E-06	mr1892_2	Jap_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