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Detailed information for vg0424199506:

Variant ID: vg0424199506 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 24199506
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.02, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

GTGCTTGAAATCAGATGGTTCCCAGTTTATATTGCTCTTCTTGCAGATCACGAATCTCTTTATCAGCTCTTCCTCAACGGGTACACAGAGATGGTCCGTT[G/A]
CCTACACAAATATAGCATTTTAGTGATTAACAAAAAAAAAGTTGAAAGAAGAGACAACGATGAATATCCGTACACTACCTATGGTTATAAATAAGCTTTC

Reverse complement sequence

GAAAGCTTATTTATAACCATAGGTAGTGTACGGATATTCATCGTTGTCTCTTCTTTCAACTTTTTTTTTGTTAATCACTAAAATGCTATATTTGTGTAGG[C/T]
AACGGACCATCTCTGTGTACCCGTTGAGGAAGAGCTGATAAAGAGATTCGTGATCTGCAAGAAGAGCAATATAAACTGGGAACCATCTGATTTCAAGCAC

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	57.20%	40.70%	0.21%	1.95%	NA
All Indica	2759	31.80%	65.60%	0.29%	2.25%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	58.70%	31.20%	0.74%	9.29%	NA
Indica I	595	4.70%	93.80%	0.00%	1.51%	NA
Indica II	465	84.10%	15.30%	0.22%	0.43%	NA
Indica III	913	20.20%	75.20%	0.55%	4.05%	NA
Indica Intermediate	786	35.00%	63.00%	0.25%	1.78%	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	67.80%	26.70%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0424199506	G -> DEL	LOC_Os04g40780.1	N	frameshift_variant	Average:35.22; most accessible tissue: Callus, score: 76.576	N	N	N	N
vg0424199506	G -> A	LOC_Os04g40780.1	missense_variant&splice_region_variant ; p.Ala308Val; MODERATE	nonsynonymous_codon ; A308V	Average:35.22; most accessible tissue: Callus, score: 76.576	benign	-1.069	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0424199506	NA	2.21E-15	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
vg0424199506	NA	1.03E-09	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
vg0424199506	NA	8.88E-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
vg0424199506	NA	5.40E-06	mr1170	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
vg0424199506	NA	4.39E-10	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
vg0424199506	NA	1.95E-06	mr1399	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
vg0424199506	NA	1.55E-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
vg0424199506	NA	8.62E-06	mr1598	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
vg0424199506	NA	3.70E-06	mr1835	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
vg0424199506	NA	1.29E-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
vg0424199506	NA	4.16E-06	mr1904	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
vg0424199506	NA	4.52E-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
vg0424199506	NA	2.20E-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
vg0424199506	NA	8.53E-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
vg0424199506	NA	5.40E-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
vg0424199506	NA	6.80E-09	mr1598_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
vg0424199506	NA	6.22E-10	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
vg0424199506	NA	8.68E-08	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
vg0424199506	NA	6.90E-16	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
vg0424199506	NA	3.46E-07	mr1904_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