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Detailed information for vg1121620131:

Variant ID: vg1121620131 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21620131
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.71, C: 0.29, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

CGAGCGGTTCTCGTCTGGACGCACGTCGTGCTAGGTCGTCTGGCTCAATGCTGTCCTTGCGGTAGACGTGTCGGACCTCGATCCCATCAAACCTTTTCTC[C/T]
AGCTTCCTGACTTCTGCGAGATACTTGGATAACTCGGGGTTAGAGCATTTATAATCTTTGTGCACCTGGTTCGCGACTAGCTCGGAGTCCCCTTTGACGA

Reverse complement sequence

TCGTCAAAGGGGACTCCGAGCTAGTCGCGAACCAGGTGCACAAAGATTATAAATGCTCTAACCCCGAGTTATCCAAGTATCTCGCAGAAGTCAGGAAGCT[G/A]
GAGAAAAGGTTTGATGGGATCGAGGTCCGACACGTCTACCGCAAGGACAGCATTGAGCCAGACGACCTAGCACGACGTGCGTCCAGACGAGAACCGCTCG

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	31.20%	2.90%	51.90%	14.05%	NA
All Indica	2759	11.10%	4.30%	74.08%	10.58%	NA
All Japonica	1512	72.50%	0.30%	5.56%	21.63%	NA
Aus	269	13.00%	3.30%	71.75%	11.90%	NA
Indica I	595	18.80%	2.20%	54.12%	24.87%	NA
Indica II	465	11.20%	4.10%	77.63%	7.10%	NA
Indica III	913	3.40%	5.90%	85.10%	5.59%	NA
Indica Intermediate	786	14.00%	4.10%	74.30%	7.63%	NA
Temperate Japonica	767	82.90%	0.10%	3.65%	13.30%	NA
Tropical Japonica	504	57.30%	0.60%	8.73%	33.33%	NA
Japonica Intermediate	241	71.00%	0.40%	4.98%	23.65%	NA
VI/Aromatic	96	3.10%	1.00%	93.75%	2.08%	NA
Intermediate	90	37.80%	3.30%	46.67%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121620131	C -> T	LOC_Os11g36640.1	synonymous_variant ; p.Leu1391Leu; LOW	synonymous_codon	Average:23.886; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg1121620131	C -> DEL	LOC_Os11g36640.1	N	frameshift_variant	Average:23.886; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121620131	1.34E-06	NA	mr1193_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
vg1121620131	7.06E-06	NA	mr1276_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
vg1121620131	2.87E-06	NA	mr1718_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