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Detailed information for vg1104448929:

Variant ID: vg1104448929 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 4448929
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.82, G: 0.20, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

ACAACCGCAGCGAGGTCATCACCAACGACCAGGGCAACCGCATCACCCCCTCCTGCGTCGCCTTCACCGCCGACGACAGGTTCGTCGGCGACGCCGCCGA[G/C]
AATCAGGCCGCCCTCAACCCCACCAACACCATCTTCGGTCATAAAACACACTCACTCGTTTATACTGCTATGCTAGCTTCTTGTTATTTTTCTTCCATCT

Reverse complement sequence

AGATGGAAGAAAAATAACAAGAAGCTAGCATAGCAGTATAAACGAGTGAGTGTGTTTTATGACCGAAGATGGTGTTGGTGGGGTTGAGGGCGGCCTGATT[C/G]
TCGGCGGCGTCGCCGACGAACCTGTCGTCGGCGGTGAAGGCGACGCAGGAGGGGGTGATGCGGTTGCCCTGGTCGTTGGTGATGACCTCGCTGCGGTTGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.80%	22.90%	7.81%	2.54%	NA
All Indica	2759	67.10%	25.00%	6.23%	1.67%	NA
All Japonica	1512	71.60%	14.50%	10.38%	3.57%	NA
Aus	269	33.50%	47.20%	12.64%	6.69%	NA
Indica I	595	45.90%	26.10%	22.69%	5.38%	NA
Indica II	465	91.60%	8.00%	0.43%	0.00%	NA
Indica III	913	61.10%	37.20%	1.20%	0.44%	NA
Indica Intermediate	786	75.40%	20.20%	3.05%	1.27%	NA
Temperate Japonica	767	54.10%	23.30%	16.69%	5.87%	NA
Tropical Japonica	504	94.80%	4.00%	0.79%	0.40%	NA
Japonica Intermediate	241	78.40%	8.30%	10.37%	2.90%	NA
VI/Aromatic	96	66.70%	31.20%	1.04%	1.04%	NA
Intermediate	90	77.80%	15.60%	5.56%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1104448929	G -> DEL	LOC_Os11g08445.1	N	frameshift_variant	Average:69.988; most accessible tissue: Minghui63 root, score: 84.069	N	N	N	N
vg1104448929	G -> C	LOC_Os11g08445.1	missense_variant ; p.Glu96Asp; MODERATE	nonsynonymous_codon ; E96D	Average:69.988; most accessible tissue: Minghui63 root, score: 84.069	benign	0.016	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1104448929	NA	3.05E-06	mr1075	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
vg1104448929	8.87E-06	8.87E-06	mr1126	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
vg1104448929	NA	6.36E-06	mr1177	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
vg1104448929	NA	1.21E-06	mr1201	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
vg1104448929	NA	1.33E-06	mr1274	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
vg1104448929	NA	1.29E-09	mr1274	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
vg1104448929	5.43E-06	5.43E-06	mr1487	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
vg1104448929	NA	3.60E-06	mr1638	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
vg1104448929	5.92E-06	NA	mr1841	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
vg1104448929	NA	1.06E-06	mr1933	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
vg1104448929	6.21E-08	3.27E-09	mr1397_2	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
vg1104448929	NA	5.47E-06	mr1508_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
vg1104448929	3.02E-06	5.30E-06	mr1843_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