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Detailed information for vg1127857666:

Variant ID: vg1127857666 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27857666
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: 272. )

Flanking Sequence (100 bp) in Reference Genome:

CAACACTGCAGACATACTTAGCATCTTCGGAAGGAAAAGGATAGAGGCCCTTTCGACACCGCCCTTTAAGAATTATGTTCCTCATGGCTCGGTCCTTAAC[C/T]
AAAAAATATTTAGAGTGAATCTCAAGAAAGACATAATTATCTTCAGCAAGGCGAGATGCAGAAATAAGATTTTTTGTAGCATGAGGAACATGAAGAACAT

Reverse complement sequence

ATGTTCTTCATGTTCCTCATGCTACAAAAAATCTTATTTCTGCATCTCGCCTTGCTGAAGATAATTATGTCTTTCTTGAGATTCACTCTAAATATTTTTT[G/A]
GTTAAGGACCGAGCCATGAGGAACATAATTCTTAAAGGGCGGTGTCGAAAGGGCCTCTATCCTTTTCCTTCCGAAGATGCTAAGTATGTCTGCAGTGTTG

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	73.30%	9.00%	4.13%	13.54%	NA
All Indica	2759	63.30%	15.00%	4.93%	16.75%	NA
All Japonica	1512	85.80%	0.30%	3.51%	10.38%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	77.10%	5.00%	6.89%	10.92%	NA
Indica II	465	65.60%	23.90%	3.01%	7.53%	NA
Indica III	913	57.50%	14.30%	4.16%	23.99%	NA
Indica Intermediate	786	58.10%	18.20%	5.47%	18.19%	NA
Temperate Japonica	767	87.40%	0.40%	2.87%	9.39%	NA
Tropical Japonica	504	85.10%	0.00%	2.58%	12.30%	NA
Japonica Intermediate	241	82.60%	0.40%	7.47%	9.54%	NA
VI/Aromatic	96	82.30%	1.00%	2.08%	14.58%	NA
Intermediate	90	84.40%	4.40%	4.44%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127857666	C -> T	LOC_Os11g46020.1	synonymous_variant ; p.Leu382Leu; LOW	synonymous_codon	Average:68.53; most accessible tissue: Zhenshan97 young leaf, score: 79.507	N	N	N	N
vg1127857666	C -> DEL	LOC_Os11g46020.1	N	frameshift_variant	Average:68.53; most accessible tissue: Zhenshan97 young leaf, score: 79.507	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127857666	NA	2.11E-07	mr1044	Ind_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
vg1127857666	8.59E-06	4.60E-08	mr1482	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
vg1127857666	6.87E-06	6.86E-06	mr1605	Ind_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