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Detailed information for vg1108050776:

Variant ID: vg1108050776 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 8050776
Reference Allele: C	Alternative Allele: T
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: 101. )

Flanking Sequence (100 bp) in Reference Genome:

TGGGTCATCGTCGATTCCTTGCAGCAAACCACCCAGTACGGAAGAAAGGCAAGCACTTCGAACATAAGGCCGACCACCGTACGAAGCCTAAACATCGCAG[C/T]
GGGAAAACAATGTTTGATATGGTTAAAGATCTTAAAGTAGTGTTCGAAAAGGGGCCTGGAAGCCAGCCTATAGAGAGCGAATATGGTCACGCGGCGATGT

Reverse complement sequence

ACATCGCCGCGTGACCATATTCGCTCTCTATAGGCTGGCTTCCAGGCCCCTTTTCGAACACTACTTTAAGATCTTTAACCATATCAAACATTGTTTTCCC[G/A]
CTGCGATGTTTAGGCTTCGTACGGTGGTCGGCCTTATGTTCGAAGTGCTTGCCTTTCTTCCGTACTGGGTGGTTTGCTGCAAGGAATCGACGATGACCCA

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	60.60%	37.20%	0.32%	1.86%	NA
All Indica	2759	37.80%	61.50%	0.47%	0.14%	NA
All Japonica	1512	93.30%	1.90%	0.00%	4.83%	NA
Aus	269	98.50%	0.40%	0.00%	1.12%	NA
Indica I	595	20.50%	78.30%	1.01%	0.17%	NA
Indica II	465	12.30%	87.30%	0.22%	0.22%	NA
Indica III	913	58.90%	40.70%	0.22%	0.11%	NA
Indica Intermediate	786	41.60%	57.80%	0.51%	0.13%	NA
Temperate Japonica	767	98.30%	1.70%	0.00%	0.00%	NA
Tropical Japonica	504	85.30%	2.60%	0.00%	12.10%	NA
Japonica Intermediate	241	94.20%	0.80%	0.00%	4.98%	NA
VI/Aromatic	96	94.80%	0.00%	0.00%	5.21%	NA
Intermediate	90	61.10%	33.30%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1108050776	C -> T	LOC_Os11g14340.1	synonymous_variant ; p.Ser452Ser; LOW	synonymous_codon	Average:31.128; most accessible tissue: Zhenshan97 flag leaf, score: 63.67	N	N	N	N
vg1108050776	C -> DEL	LOC_Os11g14340.1	N	frameshift_variant	Average:31.128; most accessible tissue: Zhenshan97 flag leaf, score: 63.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1108050776	NA	4.90E-07	mr1042	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
vg1108050776	NA	1.27E-06	mr1043	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
vg1108050776	NA	7.29E-06	mr1185	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
vg1108050776	2.61E-06	9.04E-08	mr1479	Ind_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
vg1108050776	NA	4.89E-06	mr1698	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
vg1108050776	NA	6.05E-18	mr1870	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
vg1108050776	NA	8.53E-06	mr1912	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
vg1108050776	NA	6.42E-08	mr1950	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
vg1108050776	NA	1.59E-06	mr1975	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
vg1108050776	NA	7.93E-20	mr1870_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