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Detailed information for vg0424199886:

Variant ID: vg0424199886 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 24199886
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.80, A: 0.21, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

TCTAGTAAGTGAGAACGAAGAACGAAGGCAGTACCGAAATACTAAGTATCTTCAAAAGAGGTGCTGCTTCCAAAAGAAACAGCGTCCAATTGATGCCACA[G/A]
TTTGGATGAATGCGGTGGACATCCACCAACGTCAAATTCCTCATAAAAGGAGCCAAATGTTTTGGGGTCTCCAGTTGAATCCATACCTGCATAAGATAGA

Reverse complement sequence

TCTATCTTATGCAGGTATGGATTCAACTGGAGACCCCAAAACATTTGGCTCCTTTTATGAGGAATTTGACGTTGGTGGATGTCCACCGCATTCATCCAAA[C/T]
TGTGGCATCAATTGGACGCTGTTTCTTTTGGAAGCAGCACCTCTTTTGAAGATACTTAGTATTTCGGTACTGCCTTCGTTCTTCGTTCTCACTTACTAGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.00%	38.80%	0.42%	1.76%	NA
All Indica	2759	34.80%	62.70%	0.62%	1.88%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	59.50%	29.70%	0.00%	10.78%	NA
Indica I	595	4.70%	94.10%	0.50%	0.67%	NA
Indica II	465	84.70%	14.60%	0.43%	0.22%	NA
Indica III	913	27.40%	67.70%	1.10%	3.83%	NA
Indica Intermediate	786	36.80%	61.50%	0.25%	1.53%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	72.20%	22.20%	3.33%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0424199886	G -> DEL	LOC_Os04g40780.1	N	frameshift_variant	Average:41.801; most accessible tissue: Callus, score: 66.196	N	N	N	N
vg0424199886	G -> A	LOC_Os04g40780.1	synonymous_variant ; p.Asn285Asn; LOW	synonymous_codon	Average:41.801; most accessible tissue: Callus, score: 66.196	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0424199886	NA	5.59E-14	Grain_length	Ind_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
vg0424199886	NA	3.09E-10	mr1050	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
vg0424199886	NA	2.39E-07	mr1050	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
vg0424199886	NA	4.66E-11	mr1272	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
vg0424199886	NA	7.57E-06	mr1333	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
vg0424199886	NA	6.36E-09	mr1399	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
vg0424199886	NA	6.05E-07	mr1458	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
vg0424199886	NA	6.32E-06	mr1731	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
vg0424199886	NA	5.86E-12	mr1904	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
vg0424199886	NA	1.03E-10	mr1050_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
vg0424199886	NA	1.11E-06	mr1272_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
vg0424199886	NA	7.08E-06	mr1355_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
vg0424199886	NA	4.21E-08	mr1593_2	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
vg0424199886	NA	2.31E-09	mr1835_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
vg0424199886	NA	1.04E-07	mr1895_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
vg0424199886	NA	1.15E-09	mr1902_2	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
vg0424199886	NA	4.04E-15	mr1904_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
vg0424199886	NA	5.88E-06	mr1942_2	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