Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0315357505:

Variant ID: vg0315357505 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15357505
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, A: 0.23, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

TTACGCACCAAATGTTCCGGAATAACTTGAGGAACAACTGTGCCATCTGGTTGTACATGATGAACTAAGTGTTCTGGGACAACTTGATTTGCAACATGCT[G/A]
CACGGGCTGACCACCAGGTATCGTAAACCCAGCCGATGCATTCATCGGACCTTGCTGCTGAATCGGCTGAACGACCTGTTGCCTTAGTGGCGTCTGCTGA

Reverse complement sequence

TCAGCAGACGCCACTAAGGCAACAGGTCGTTCAGCCGATTCAGCAGCAAGGTCCGATGAATGCATCGGCTGGGTTTACGATACCTGGTGGTCAGCCCGTG[C/T]
AGCATGTTGCAAATCAAGTTGTCCCAGAACACTTAGTTCATCATGTACAACCAGATGGCACAGTTGTTCCTCAAGTTATTCCGGAACATTTGGTGCGTAA

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	92.90%	7.00%	0.08%	0.04%	NA
All Indica	2759	95.70%	4.20%	0.11%	0.04%	NA
All Japonica	1512	91.30%	8.70%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	93.10%	6.70%	0.00%	0.22%	NA
Indica III	913	91.70%	8.20%	0.11%	0.00%	NA
Indica Intermediate	786	98.60%	1.10%	0.25%	0.00%	NA
Temperate Japonica	767	91.90%	8.10%	0.00%	0.00%	NA
Tropical Japonica	504	92.90%	7.10%	0.00%	0.00%	NA
Japonica Intermediate	241	85.90%	14.10%	0.00%	0.00%	NA
VI/Aromatic	96	18.80%	80.20%	1.04%	0.00%	NA
Intermediate	90	93.30%	5.60%	0.00%	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
vg0315357505	G -> A	LOC_Os03g26900.1	stop_gained ; p.Gln200*; HIGH	stop_gained	Average:57.767; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N
vg0315357505	G -> DEL	LOC_Os03g26900.1	N	frameshift_variant	Average:57.767; most accessible tissue: Minghui63 flag leaf, score: 77.494	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315357505	8.61E-06	NA	mr1023_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
vg0315357505	4.20E-06	NA	mr1023_2	Jap_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
vg0315357505	NA	1.73E-08	mr1057_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
vg0315357505	7.77E-06	NA	mr1489_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
vg0315357505	NA	1.32E-06	mr1613_2	Jap_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
vg0315357505	7.86E-07	NA	mr1778_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
vg0315357505	NA	2.01E-06	mr1913_2	Jap_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