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Detailed information for vg1121617585:

Variant ID: vg1121617585 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21617585
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.88, T: 0.12, others allele: 0.00, population size: 43. )

Flanking Sequence (100 bp) in Reference Genome:

TGCAGCTTGACTTAGTGGTTATCACATTAAGAAGATCTCGAGGGTGCCCTTGCTGGCCAAGATCATCGTATCCAATACTGGAAGATGAAGTTTGAAGTGG[C/T]
GGAACTCGAGAGAACCATGCTGGCAGTGAAGAAAGAGCAGGCTGTGGAAACGCTCCAAGGTCGCGAGGTGTGGTTTAACTCGTACTTGAAGAGTTGCTGC

Reverse complement sequence

GCAGCAACTCTTCAAGTACGAGTTAAACCACACCTCGCGACCTTGGAGCGTTTCCACAGCCTGCTCTTTCTTCACTGCCAGCATGGTTCTCTCGAGTTCC[G/A]
CCACTTCAAACTTCATCTTCCAGTATTGGATACGATGATCTTGGCCAGCAAGGGCACCCTCGAGATCTTCTTAATGTGATAACCACTAAGTCAAGCTGCA

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	62.90%	21.30%	6.58%	9.29%	NA
All Indica	2759	55.50%	33.50%	7.61%	3.44%	NA
All Japonica	1512	73.60%	3.20%	3.90%	19.31%	NA
Aus	269	85.50%	1.90%	10.41%	2.23%	NA
Indica I	595	66.10%	12.80%	14.79%	6.39%	NA
Indica II	465	37.00%	54.40%	6.24%	2.37%	NA
Indica III	913	57.90%	35.80%	4.27%	1.97%	NA
Indica Intermediate	786	55.50%	34.10%	6.87%	3.56%	NA
Temperate Japonica	767	83.20%	1.30%	3.52%	11.99%	NA
Tropical Japonica	504	61.10%	6.30%	5.75%	26.79%	NA
Japonica Intermediate	241	69.30%	2.50%	1.24%	26.97%	NA
VI/Aromatic	96	45.80%	16.70%	7.29%	30.21%	NA
Intermediate	90	60.00%	13.30%	7.78%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121617585	C -> T	LOC_Os11g36630.1	missense_variant ; p.Ala578Val; MODERATE	nonsynonymous_codon ; A578V	Average:12.773; most accessible tissue: Minghui63 root, score: 25.504	benign	0.448	TOLERATED	0.06
vg1121617585	C -> DEL	LOC_Os11g36630.1	N	frameshift_variant	Average:12.773; most accessible tissue: Minghui63 root, score: 25.504	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121617585	3.94E-06	5.79E-10	mr1053	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
vg1121617585	1.71E-06	4.54E-07	mr1053	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
vg1121617585	4.37E-06	NA	mr1128	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
vg1121617585	1.08E-06	1.51E-06	mr1128	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
vg1121617585	9.13E-06	NA	mr1139	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
vg1121617585	8.07E-06	9.87E-06	mr1139	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
vg1121617585	5.90E-06	3.94E-06	mr1147	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
vg1121617585	NA	6.39E-06	mr1204	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
vg1121617585	NA	6.70E-06	mr1437	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
vg1121617585	NA	4.75E-10	mr1709	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
vg1121617585	NA	2.82E-09	mr1709	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
vg1121617585	NA	9.49E-06	mr1772	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
vg1121617585	7.01E-06	NA	mr1913	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
vg1121617585	NA	3.35E-06	mr1956	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