Search for Variation information by Variation ID:

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

Detailed information for vg0320620607:

Variant ID: vg0320620607 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 20620607
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.01, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

GATGAAGCAAGCAGCAAGGGAACTCCACCACCCAAGGGAGCTACTATACCTTTTGATTATAGCAAACTTACCATTCCTTCTCACAACTTCGTCTCCGTGC[C/A]
TTCCGGGCGTGCTCCTCAATTTGATGGGACATATTATGCCGCTTGGAAGCACAAGATGAAGTTGCATCTAATCTCTTTGCATCCAAATATTTGGAAAGTT

Reverse complement sequence

AACTTTCCAAATATTTGGATGCAAAGAGATTAGATGCAACTTCATCTTGTGCTTCCAAGCGGCATAATATGTCCCATCAAATTGAGGAGCACGCCCGGAA[G/T]
GCACGGAGACGAAGTTGTGAGAAGGAATGGTAAGTTTGCTATAATCAAAAGGTATAGTAGCTCCCTTGGGTGGTGGAGTTCCCTTGCTGCTTGCTTCATC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.30%	15.40%	1.04%	46.30%	NA
All Indica	2759	7.80%	20.10%	1.20%	70.86%	NA
All Japonica	1512	87.50%	10.90%	0.66%	0.93%	NA
Aus	269	33.80%	0.00%	1.86%	64.31%	NA
Indica I	595	5.00%	5.90%	2.02%	87.06%	NA
Indica II	465	8.40%	23.90%	1.08%	66.67%	NA
Indica III	913	6.50%	30.70%	0.55%	62.32%	NA
Indica Intermediate	786	11.20%	16.40%	1.40%	70.99%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	66.50%	29.60%	1.98%	1.98%	NA
Japonica Intermediate	241	92.50%	6.60%	0.00%	0.83%	NA
VI/Aromatic	96	81.20%	0.00%	0.00%	18.75%	NA
Intermediate	90	58.90%	8.90%	1.11%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0320620607	C -> A	LOC_Os03g37210.1	missense_variant ; p.Pro48His; MODERATE	nonsynonymous_codon ; P48H	Average:19.659; most accessible tissue: Minghui63 young leaf, score: 44.63	probably damaging	3.126	DELETERIOUS	0.03
vg0320620607	C -> DEL	LOC_Os03g37210.1	N	frameshift_variant	Average:19.659; most accessible tissue: Minghui63 young leaf, score: 44.63	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0320620607	NA	6.13E-07	mr1136	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
vg0320620607	NA	5.48E-09	mr1217	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
vg0320620607	NA	3.24E-06	mr1227	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
vg0320620607	2.89E-10	8.55E-12	mr1439	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
vg0320620607	2.33E-06	2.29E-08	mr1439	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
vg0320620607	4.84E-06	4.84E-06	mr1494	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
vg0320620607	NA	3.93E-06	mr1583	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
vg0320620607	1.39E-06	NA	mr1836	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
vg0320620607	4.70E-06	4.70E-06	mr1836	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
vg0320620607	NA	4.88E-08	mr1845	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
vg0320620607	2.62E-07	2.30E-09	mr1852	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
vg0320620607	NA	2.02E-08	mr1852	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
vg0320620607	NA	8.95E-09	mr1136_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