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Detailed information for vg0804931252:

Variant ID: vg0804931252 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4931252
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, C: 0.33, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

CGGCGTGGTTGCTCCACTGGACCTTGCAAAAACGGATTACCCGGTTCCTGGTCCTGCGCTCCATGGTGTCCAGGATTTTCACTGGCTTCTCCACATACGT[T/C]
AAATCTTCGCGAACTTCAATTTGCTCTGAGTCGGCCTGCTCGGATGGCACTCGAAGGCATTTCTTGAGTTGCGACACATGGAACACATCATGCACGTTGC

Reverse complement sequence

GCAACGTGCATGATGTGTTCCATGTGTCGCAACTCAAGAAATGCCTTCGAGTGCCATCCGAGCAGGCCGACTCAGAGCAAATTGAAGTTCGCGAAGATTT[A/G]
ACGTATGTGGAGAAGCCAGTGAAAATCCTGGACACCATGGAGCGCAGGACCAGGAACCGGGTAATCCGTTTTTGCAAGGTCCAGTGGAGCAACCACGCCG

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	55.40%	18.50%	25.33%	0.76%	NA
All Indica	2759	86.50%	2.40%	11.05%	0.04%	NA
All Japonica	1512	5.00%	52.50%	40.21%	2.31%	NA
Aus	269	34.20%	0.00%	65.80%	0.00%	NA
Indica I	595	93.60%	2.90%	3.36%	0.17%	NA
Indica II	465	74.00%	5.20%	20.86%	0.00%	NA
Indica III	913	91.90%	0.70%	7.45%	0.00%	NA
Indica Intermediate	786	82.20%	2.50%	15.27%	0.00%	NA
Temperate Japonica	767	4.80%	87.40%	6.65%	1.17%	NA
Tropical Japonica	504	4.80%	6.50%	85.52%	3.17%	NA
Japonica Intermediate	241	5.80%	37.80%	52.28%	4.15%	NA
VI/Aromatic	96	19.80%	1.00%	79.17%	0.00%	NA
Intermediate	90	52.20%	13.30%	34.44%	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
vg0804931252	T -> C	LOC_Os08g08550.1	synonymous_variant ; p.Leu1723Leu; LOW	synonymous_codon	Average:20.33; most accessible tissue: Minghui63 flag leaf, score: 28.781	N	N	N	N
vg0804931252	T -> DEL	LOC_Os08g08550.1	N	frameshift_variant	Average:20.33; most accessible tissue: Minghui63 flag leaf, score: 28.781	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804931252	NA	9.06E-06	mr1047	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
vg0804931252	NA	6.86E-09	mr1162	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
vg0804931252	NA	2.67E-11	mr1471	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
vg0804931252	8.85E-06	NA	mr1498	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
vg0804931252	NA	1.50E-06	mr1587	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
vg0804931252	NA	3.39E-06	mr1704	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
vg0804931252	NA	1.72E-09	mr1722	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
vg0804931252	NA	1.89E-07	mr1815	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
vg0804931252	NA	4.49E-06	mr1555_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
vg0804931252	NA	1.00E-07	mr1748_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