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Detailed information for vg1116350295:

Variant ID: vg1116350295 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16350295
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.52, C: 0.49, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

TTAGATGAAGATCAATCTAAAGTGGCTATGGGAGAGGTGAATGAAGGAATTTGTGGAACTCATCAATCGGCCCATAAGATAAATTGGTTGCTTAGAAGAG[T/C]
GGGGTTCTATTGGCCGAAGATGATTGATGATTGCTTCAAATATTATAGAGGATGCGAGGCTTGTCAACGGTTCGGCAATGTTCAATTGGCGCCCGCCGCC

Reverse complement sequence

GGCGGCGGGCGCCAATTGAACATTGCCGAACCGTTGACAAGCCTCGCATCCTCTATAATATTTGAAGCAATCATCAATCATCTTCGGCCAATAGAACCCC[A/G]
CTCTTCTAAGCAACCAATTTATCTTATGGGCCGATTGATGAGTTCCACAAATTCCTTCATTCACCTCTCCCATAGCCACTTTAGATTGATCTTCATCTAA

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	29.10%	7.30%	50.53%	13.06%	NA
All Indica	2759	12.90%	10.50%	74.66%	1.92%	NA
All Japonica	1512	54.80%	2.20%	6.22%	36.71%	NA
Aus	269	27.50%	5.20%	67.29%	0.00%	NA
Indica I	595	4.00%	10.10%	84.54%	1.34%	NA
Indica II	465	17.00%	6.00%	76.13%	0.86%	NA
Indica III	913	14.20%	15.40%	69.99%	0.33%	NA
Indica Intermediate	786	15.60%	7.80%	71.76%	4.83%	NA
Temperate Japonica	767	83.80%	1.00%	2.22%	12.91%	NA
Tropical Japonica	504	25.20%	3.60%	12.70%	58.53%	NA
Japonica Intermediate	241	24.50%	3.30%	5.39%	66.80%	NA
VI/Aromatic	96	91.70%	2.10%	6.25%	0.00%	NA
Intermediate	90	32.20%	5.60%	52.22%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116350295	T -> DEL	LOC_Os11g28410.1	N	frameshift_variant	Average:17.679; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg1116350295	T -> C	LOC_Os11g28410.1	missense_variant ; p.Val285Ala; MODERATE	nonsynonymous_codon ; V285A	Average:17.679; most accessible tissue: Zhenshan97 panicle, score: 24.575	benign	-0.338	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116350295	1.05E-06	1.05E-06	mr1164	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
vg1116350295	NA	1.72E-07	mr1229	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