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Detailed information for vg1109209726:

Variant ID: vg1109209726 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9209726
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: 222. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTCCTTTTGGGTATAACCCTTGGCCACAAGTCTTGCCTTGTACTTTTCAATTGTACCATCAGGCCGAAGCTTTTTCTTGAAAACTCATTTGCATCCTA[C/T]
GGGCTTGCACCCATATGGACGCTCAACGACTTCCCAAGTGCCATTAGACATAATCGAGTCCATCTCACTGCGTACTGCTTCCTTCCAGTAGTCAGCGTCA

Reverse complement sequence

TGACGCTGACTACTGGAAGGAAGCAGTACGCAGTGAGATGGACTCGATTATGTCTAATGGCACTTGGGAAGTCGTTGAGCGTCCATATGGGTGCAAGCCC[G/A]
TAGGATGCAAATGAGTTTTCAAGAAAAAGCTTCGGCCTGATGGTACAATTGAAAAGTACAAGGCAAGACTTGTGGCCAAGGGTTATACCCAAAAGGAAGG

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	61.90%	31.50%	6.67%	0.00%	NA
All Indica	2759	37.40%	52.00%	10.66%	0.00%	NA
All Japonica	1512	97.70%	1.90%	0.46%	0.00%	NA
Aus	269	94.40%	2.20%	3.35%	0.00%	NA
Indica I	595	13.10%	73.90%	12.94%	0.00%	NA
Indica II	465	61.50%	28.40%	10.11%	0.00%	NA
Indica III	913	39.40%	53.70%	6.90%	0.00%	NA
Indica Intermediate	786	39.10%	47.30%	13.61%	0.00%	NA
Temperate Japonica	767	97.40%	1.80%	0.78%	0.00%	NA
Tropical Japonica	504	97.60%	2.20%	0.20%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	75.60%	18.90%	5.56%	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
vg1109209726	C -> T	LOC_Os11g16610.1	splice_donor_variant&intron_variant ; HIGH	splice_donor_variant	Average:19.232; most accessible tissue: Minghui63 young leaf, score: 44.63	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109209726	NA	1.89E-07	mr1053	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
vg1109209726	NA	5.07E-06	mr1077	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
vg1109209726	NA	5.89E-06	mr1135	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
vg1109209726	NA	9.55E-06	mr1482	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
vg1109209726	NA	1.76E-07	mr1504	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
vg1109209726	NA	4.48E-06	mr1715	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
vg1109209726	NA	6.25E-09	mr1837	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
vg1109209726	1.88E-06	2.44E-08	mr1837	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