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Detailed information for vg1116465115:

Variant ID: vg1116465115 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16465115
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCTACAACACATGGTTTCTTAAAGTGGTCCATTAATAAATACATCATCTCTCTTCTGTACCAATCATATTTATTCTTCATATATTATGAAGACACTATT[A/C]
TTTACCAATGCAAAACTTGATAGTGTCTAGTGCATAGGTTCTCGTGTTGAAGCTGTCTCTTGCATGAGACCCAGTTTTTTCCTCTCTTCACTATCTCTCT

Reverse complement sequence

AGAGAGATAGTGAAGAGAGGAAAAAACTGGGTCTCATGCAAGAGACAGCTTCAACACGAGAACCTATGCACTAGACACTATCAAGTTTTGCATTGGTAAA[T/G]
AATAGTGTCTTCATAATATATGAAGAATAAATATGATTGGTACAGAAGAGAGATGATGTATTTATTAATGGACCACTTTAAGAAACCATGTGTTGTAGAG

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	65.50%	34.20%	0.34%	0.00%	NA
All Indica	2759	98.40%	1.20%	0.33%	0.00%	NA
All Japonica	1512	4.40%	95.40%	0.26%	0.00%	NA
Aus	269	93.30%	6.70%	0.00%	0.00%	NA
Indica I	595	98.80%	0.80%	0.34%	0.00%	NA
Indica II	465	99.10%	0.40%	0.43%	0.00%	NA
Indica III	913	99.20%	0.70%	0.11%	0.00%	NA
Indica Intermediate	786	96.80%	2.70%	0.51%	0.00%	NA
Temperate Japonica	767	2.90%	96.90%	0.26%	0.00%	NA
Tropical Japonica	504	6.90%	92.70%	0.40%	0.00%	NA
Japonica Intermediate	241	3.70%	96.30%	0.00%	0.00%	NA
VI/Aromatic	96	10.40%	88.50%	1.04%	0.00%	NA
Intermediate	90	57.80%	40.00%	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
vg1116465115	A -> C	LOC_Os11g28550.1	downstream_gene_variant ; 3321.0bp to feature; MODIFIER	silent_mutation	Average:43.447; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg1116465115	A -> C	LOC_Os11g28540-LOC_Os11g28550	intergenic_region ; MODIFIER	silent_mutation	Average:43.447; 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
vg1116465115	NA	5.35E-19	Yield	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1116465115	NA	1.73E-78	mr1135	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
vg1116465115	NA	6.24E-24	mr1375	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
vg1116465115	NA	3.18E-23	mr1383	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
vg1116465115	NA	2.50E-87	mr1504	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
vg1116465115	NA	7.68E-89	mr1517	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
vg1116465115	NA	1.48E-88	mr1672	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
vg1116465115	NA	1.39E-21	mr1698	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
vg1116465115	3.62E-07	5.07E-103	mr1758	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
vg1116465115	1.18E-06	1.18E-06	mr1758	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
vg1116465115	NA	6.81E-07	mr1797	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
vg1116465115	NA	6.81E-07	mr1801	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
vg1116465115	NA	1.30E-40	mr1873	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
vg1116465115	NA	2.29E-38	mr1541_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
vg1116465115	5.59E-11	2.19E-147	mr1758_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
vg1116465115	9.41E-09	5.28E-12	mr1758_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