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Detailed information for vg1104295774:

Variant ID: vg1104295774 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 4295774
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

GAGCAATCTTCAATGCAACCATGTCGTTTTGGTTTCAGTGCATCTATTGATGAGTTCTTTTTTTGTCAACCTTTTCTAATCAACACAGGTACCACACGTG[C/T]
TGTACAAGCCAACCCCAAAGAAGCTGGTGACCTGTGCCGACTCACTCTGCACTGACCTGTACACTGATCTGGGCAAGCCCAAGAGATGTGGATCCCAGAA

Reverse complement sequence

TTCTGGGATCCACATCTCTTGGGCTTGCCCAGATCAGTGTACAGGTCAGTGCAGAGTGAGTCGGCACAGGTCACCAGCTTCTTTGGGGTTGGCTTGTACA[G/A]
CACGTGTGGTACCTGTGTTGATTAGAAAAGGTTGACAAAAAAAGAACTCATCAATAGATGCACTGAAACCAAAACGACATGGTTGCATTGAAGATTGCTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.30%	38.70%	0.00%	0.00%	NA
All Indica	2759	89.50%	10.50%	0.00%	0.00%	NA
All Japonica	1512	11.50%	88.50%	0.00%	0.00%	NA
Aus	269	42.40%	57.60%	0.00%	0.00%	NA
Indica I	595	80.50%	19.50%	0.00%	0.00%	NA
Indica II	465	95.10%	4.90%	0.00%	0.00%	NA
Indica III	913	91.60%	8.40%	0.00%	0.00%	NA
Indica Intermediate	786	90.50%	9.50%	0.00%	0.00%	NA
Temperate Japonica	767	1.20%	98.80%	0.00%	0.00%	NA
Tropical Japonica	504	29.20%	70.80%	0.00%	0.00%	NA
Japonica Intermediate	241	7.50%	92.50%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	63.30%	36.70%	0.00%	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
vg1104295774	C -> T	LOC_Os11g08200.1	synonymous_variant ; p.Leu80Leu; LOW	synonymous_codon	Average:38.232; most accessible tissue: Callus, score: 86.522	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1104295774	NA	7.45E-06	mr1127	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
vg1104295774	2.12E-08	1.24E-10	mr1218	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
vg1104295774	1.95E-06	1.68E-08	mr1522	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
vg1104295774	NA	1.88E-06	mr1553	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
vg1104295774	NA	2.26E-06	mr1571	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
vg1104295774	NA	4.78E-08	mr1583	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
vg1104295774	NA	1.52E-06	mr1622	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
vg1104295774	NA	6.94E-06	mr1622	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
vg1104295774	3.03E-18	3.16E-58	mr1638	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
vg1104295774	7.91E-10	1.01E-12	mr1638	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
vg1104295774	2.48E-06	1.13E-08	mr1638	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
vg1104295774	NA	2.92E-07	mr1218_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
vg1104295774	NA	9.76E-08	mr1850_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