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Detailed information for vg1118496921:

Variant ID: vg1118496921 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18496921
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.01, others allele: 0.00, population size: 354. )

Flanking Sequence (100 bp) in Reference Genome:

GCTGTTGCGGATGGAAATGCAGATCTACAAGGAAAAGAATCAAATGTTAGATATTAATGCCTGAAACTAATGATGCTTCAGCAGCGGGGAAGTGGCCAAG[C/A]
TTTATCCGTGACCGGGAGCAGTTGGAAGAGTGTAGGCACGCATCGGAATCAAGATTTATGGCCTAATCCAGAGAGAAGATAATGGTGGCATAGAAGCTTA

Reverse complement sequence

TAAGCTTCTATGCCACCATTATCTTCTCTCTGGATTAGGCCATAAATCTTGATTCCGATGCGTGCCTACACTCTTCCAACTGCTCCCGGTCACGGATAAA[G/T]
CTTGGCCACTTCCCCGCTGCTGAAGCATCATTAGTTTCAGGCATTAATATCTAACATTTGATTCTTTTCCTTGTAGATCTGCATTTCCATCCGCAACAGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.40%	2.80%	0.80%	0.00%	NA
All Indica	2759	99.70%	0.10%	0.18%	0.00%	NA
All Japonica	1512	90.80%	7.10%	2.12%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.00%	0.38%	0.00%	NA
Temperate Japonica	767	93.40%	3.40%	3.26%	0.00%	NA
Tropical Japonica	504	95.40%	4.40%	0.20%	0.00%	NA
Japonica Intermediate	241	73.00%	24.50%	2.49%	0.00%	NA
VI/Aromatic	96	77.10%	21.90%	1.04%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg1118496921	C -> A	LOC_Os11g31630.1	intron_variant ; MODIFIER	silent_mutation	Average:72.41; most accessible tissue: Minghui63 flag leaf, score: 87.594	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1118496921	1.35E-06	1.35E-06	mr1648_2	Jap_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
vg1118496921	NA	6.97E-06	mr1691_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
vg1118496921	NA	3.68E-07	mr1851_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