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Detailed information for vg1121750233:

Variant ID: vg1121750233 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21750233
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.73, C: 0.28, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

CACCCTTGCTGTTTAATTTAGCAGCAGAAACACTCACCTTGTTGGTGCAAAGGGCTGAGAGCAGTTCCCTTTTGGAGGGTTTGTCAGTTAGTGAGAACAA[T/C]
AAGGTGACAATTCTGAAGTATGCTGATGACACGATATTTATGATCAAAGACAATGTGGAGCAAGCTAGAAACCTGAAATTCATCCTGTGCCTTTTTGAAC

Reverse complement sequence

GTTCAAAAAGGCACAGGATGAATTTCAGGTTTCTAGCTTGCTCCACATTGTCTTTGATCATAAATATCGTGTCATCAGCATACTTCAGAATTGTCACCTT[A/G]
TTGTTCTCACTAACTGACAAACCCTCCAAAAGGGAACTGCTCTCAGCCCTTTGCACCAACAAGGTGAGTGTTTCTGCTGCTAAATTAAACAGCAAGGGTG

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	48.70%	37.90%	0.72%	12.67%	NA
All Indica	2759	71.30%	10.50%	0.94%	17.22%	NA
All Japonica	1512	6.30%	92.00%	0.07%	1.59%	NA
Aus	269	67.70%	20.80%	0.00%	11.52%	NA
Indica I	595	77.30%	2.40%	1.01%	19.33%	NA
Indica II	465	70.80%	3.00%	2.15%	24.09%	NA
Indica III	913	68.00%	20.00%	0.11%	11.83%	NA
Indica Intermediate	786	70.90%	10.20%	1.15%	17.81%	NA
Temperate Japonica	767	7.80%	91.50%	0.00%	0.65%	NA
Tropical Japonica	504	5.20%	91.90%	0.20%	2.78%	NA
Japonica Intermediate	241	4.10%	93.80%	0.00%	2.07%	NA
VI/Aromatic	96	13.50%	22.90%	3.12%	60.42%	NA
Intermediate	90	46.70%	36.70%	4.44%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121750233	T -> DEL	LOC_Os11g36870.1	N	frameshift_variant	Average:25.865; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N
vg1121750233	T -> C	LOC_Os11g36870.1	synonymous_variant ; p.Asn854Asn; LOW	synonymous_codon	Average:25.865; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121750233	NA	2.45E-08	mr1162	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
vg1121750233	7.95E-06	7.95E-06	mr1162	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