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Detailed information for vg1116239941:

Variant ID: vg1116239941 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16239941
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.70, T: 0.30, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

GCACTTCTTCGACAGCCATCACAGCCTTGCCCGCCCGATCTGTTCTGAACTTTCTCCAAGTCATGGGGGCTTGGCCTTGCCTTGGCGGCTGTCCCTGGAT[T/C]
GCCGGCTGAGACTGGCGAACAGAGAGGGGAGGTGGTTCGGCAATTTGAACTTGTGCTTGAGCTTGAGCAGCGGCGACGGAGGCTTTATCGTACTCAGCTT

Reverse complement sequence

AAGCTGAGTACGATAAAGCCTCCGTCGCCGCTGCTCAAGCTCAAGCACAAGTTCAAATTGCCGAACCACCTCCCCTCTCTGTTCGCCAGTCTCAGCCGGC[A/G]
ATCCAGGGACAGCCGCCAAGGCAAGGCCAAGCCCCCATGACTTGGAGAAAGTTCAGAACAGATCGGGCGGGCAAGGCTGTGATGGCTGTCGAAGAAGTGC

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	63.90%	34.40%	1.08%	0.57%	NA
All Indica	2759	98.10%	1.40%	0.54%	0.00%	NA
All Japonica	1512	3.40%	96.60%	0.00%	0.00%	NA
Aus	269	74.70%	1.90%	13.38%	10.04%	NA
Indica I	595	97.10%	2.20%	0.67%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	96.60%	2.00%	1.40%	0.00%	NA
Temperate Japonica	767	3.30%	96.70%	0.00%	0.00%	NA
Tropical Japonica	504	4.00%	96.00%	0.00%	0.00%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	56.70%	43.30%	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
vg1116239941	T -> DEL	LOC_Os11g28250.1	N	frameshift_variant	Average:23.774; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N
vg1116239941	T -> C	LOC_Os11g28250.1	synonymous_variant ; p.Ala547Ala; LOW	synonymous_codon	Average:23.774; most accessible tissue: Zhenshan97 flag leaf, score: 49.013	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116239941	NA	1.05E-18	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
vg1116239941	NA	2.03E-75	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
vg1116239941	NA	3.72E-23	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
vg1116239941	NA	1.48E-22	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
vg1116239941	NA	2.20E-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
vg1116239941	NA	3.46E-68	mr1538	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
vg1116239941	NA	1.77E-56	mr1594	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
vg1116239941	NA	4.74E-86	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
vg1116239941	3.01E-15	1.19E-116	mr1758	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
vg1116239941	8.61E-07	8.61E-07	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
vg1116239941	NA	6.39E-40	mr1891	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
vg1116239941	NA	1.04E-15	mr1162_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
vg1116239941	1.36E-11	1.51E-157	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
vg1116239941	NA	4.52E-09	mr1758_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