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Detailed information for vg0410309978:

Variant ID: vg0410309978 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 10309978
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:

CGAAGGGGTACGAAGGGTGCTTGAATAGATGTCAAAATGTTCGGTCCTTAACGACTCAGACCGGGCTACTTGCATCAGAGGAAAACCAACCTCCCTTCAT[T/C]
GCCCTATCACCCGTCCAAGTCCAACATATTTCATCAACCATTATTTAGCGTAAGTGCTCAAGTTTTATGCCCAATAATGCAAGTTGTCTATATACCACAA

Reverse complement sequence

TTGTGGTATATAGACAACTTGCATTATTGGGCATAAAACTTGAGCACTTACGCTAAATAATGGTTGATGAAATATGTTGGACTTGGACGGGTGATAGGGC[A/G]
ATGAAGGGAGGTTGGTTTTCCTCTGATGCAAGTAGCCCGGTCTGAGTCGTTAAGGACCGAACATTTTGACATCTATTCAAGCACCCTTCGTACCCCTTCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.50%	20.40%	0.51%	2.60%	NA
All Indica	2759	99.20%	0.80%	0.00%	0.04%	NA
All Japonica	1512	33.90%	61.00%	1.46%	3.64%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	98.60%	1.30%	0.00%	0.13%	NA
Temperate Japonica	767	3.70%	96.00%	0.13%	0.26%	NA
Tropical Japonica	504	83.30%	4.40%	3.77%	8.53%	NA
Japonica Intermediate	241	27.00%	68.00%	0.83%	4.15%	NA
VI/Aromatic	96	33.30%	0.00%	2.08%	64.58%	NA
Intermediate	90	74.40%	20.00%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0410309978	T -> C	LOC_Os04g18640.1	upstream_gene_variant ; 2450.0bp to feature; MODIFIER	silent_mutation	Average:43.75; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N
vg0410309978	T -> C	LOC_Os04g18640-LOC_Os04g18650	intergenic_region ; MODIFIER	silent_mutation	Average:43.75; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N
vg0410309978	T -> DEL	N	N	silent_mutation	Average:43.75; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0410309978	NA	2.58E-07	mr1194	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
vg0410309978	NA	2.18E-34	mr1310	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
vg0410309978	NA	3.74E-08	mr1449	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
vg0410309978	NA	2.12E-11	mr1650	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
vg0410309978	NA	5.08E-07	mr1715	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
vg0410309978	NA	8.71E-09	mr1746	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
vg0410309978	NA	2.46E-31	mr1789	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
vg0410309978	NA	6.15E-13	mr1844	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
vg0410309978	NA	2.06E-40	mr1926	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
vg0410309978	NA	8.30E-11	mr1959	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
vg0410309978	NA	6.41E-06	mr1211_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
vg0410309978	NA	5.82E-10	mr1282_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
vg0410309978	3.71E-08	NA	mr1758_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