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Detailed information for vg1102888595:

Variant ID: vg1102888595 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 2888595
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

TATCTGTCAAATCTACCTTTTAGGTCAATTTTGTGTGTATGCCCTTTTTATGAAGTTAACACATAATTATATCTATCTAGTGCATGAGTGTTGAGACTGC[C/T]
TTAATTCTCTTGTTGATCAAGTAAAGTATATACGTTTTTCTTGCTTTATCTTGGCGACTTGGCCATGTTCTACCTTGCTCCTTGGTTTATCTTCCAGAGC

Reverse complement sequence

GCTCTGGAAGATAAACCAAGGAGCAAGGTAGAACATGGCCAAGTCGCCAAGATAAAGCAAGAAAAACGTATATACTTTACTTGATCAACAAGAGAATTAA[G/A]
GCAGTCTCAACACTCATGCACTAGATAGATATAATTATGTGTTAACTTCATAAAAAGGGCATACACACAAAATTGACCTAAAAGGTAGATTTGACAGATA

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	95.10%	3.60%	1.29%	0.00%	NA
All Indica	2759	99.40%	0.10%	0.47%	0.00%	NA
All Japonica	1512	86.10%	10.80%	3.04%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.30%	0.50%	1.18%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.00%	0.64%	0.00%	NA
Temperate Japonica	767	77.80%	16.90%	5.22%	0.00%	NA
Tropical Japonica	504	99.60%	0.00%	0.40%	0.00%	NA
Japonica Intermediate	241	84.20%	14.10%	1.66%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	2.22%	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
vg1102888595	C -> T	LOC_Os11g06050-LOC_Os11g06070	intergenic_region ; MODIFIER	silent_mutation	Average:45.242; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1102888595	1.77E-06	1.77E-06	mr1499_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
vg1102888595	8.13E-07	8.13E-07	mr1616_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