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Detailed information for vg1121816844:

Variant ID: vg1121816844 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21816844
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.86, T: 0.14, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

TTATTCATCTAAAATTCTGTCAATGTCATTTCGAAAGAATAGACCTGACTGGGGTTTTGAAATAGAATGTGGTACTTACTTTTTATGATAATCTGAGTGG[C/T]
ACATTGTTTTTACAGAAATGATGAATGCCCAGCATGCCGCACCCCTGCAAGTAGTCATTCCTTGAAGGTTGATCCTAATTTTGATGCTTTAATTTTGACG

Reverse complement sequence

CGTCAAAATTAAAGCATCAAAATTAGGATCAACCTTCAAGGAATGACTACTTGCAGGGGTGCGGCATGCTGGGCATTCATCATTTCTGTAAAAACAATGT[G/A]
CCACTCAGATTATCATAAAAAGTAAGTACCACATTCTATTTCAAAACCCCAGTCAGGTCTATTCTTTCGAAATGACATTGACAGAATTTTAGATGAATAA

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	31.10%	13.00%	3.05%	52.90%	NA
All Indica	2759	11.90%	18.60%	1.85%	67.60%	NA
All Japonica	1512	68.70%	1.40%	2.25%	27.65%	NA
Aus	269	24.20%	0.40%	19.70%	55.76%	NA
Indica I	595	2.40%	22.90%	1.85%	72.94%	NA
Indica II	465	2.40%	31.00%	1.51%	65.16%	NA
Indica III	913	24.00%	7.40%	2.30%	66.27%	NA
Indica Intermediate	786	10.80%	21.10%	1.53%	66.54%	NA
Temperate Japonica	767	78.70%	1.20%	3.00%	17.08%	NA
Tropical Japonica	504	58.70%	1.20%	1.39%	38.69%	NA
Japonica Intermediate	241	57.70%	2.50%	1.66%	38.17%	NA
VI/Aromatic	96	6.20%	66.70%	1.04%	26.04%	NA
Intermediate	90	33.30%	14.40%	5.56%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121816844	C -> T	LOC_Os11g36970.1	intron_variant ; MODIFIER	silent_mutation	Average:26.194; most accessible tissue: Callus, score: 42.376	N	N	N	N
vg1121816844	C -> DEL	N	N	silent_mutation	Average:26.194; most accessible tissue: Callus, score: 42.376	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121816844	NA	3.15E-07	mr1545_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