Search for Variation information by Variation ID:

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

Detailed information for vg1023134528:

Variant ID: vg1023134528 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 23134528
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTGCAATAGTTGGTTTGTCGATAGACACAAAGAGGCAACTGTAGATATCCTGAGTGGAAAGAAGTGGCCCACAAAAGTTAAGGACATGTTGGAGGAGCA[A/G]
CAAAGACGAACCTTGGGGCAAAGAGCAGCATGTTTTGATTTCCCTTCGATGAAGTATGAGGTCAGCGAGCAAGGCGGAGTCACGGCGGCTGGGGTTCAAT

Reverse complement sequence

ATTGAACCCCAGCCGCCGTGACTCCGCCTTGCTCGCTGACCTCATACTTCATCGAAGGGAAATCAAAACATGCTGCTCTTTGCCCCAAGGTTCGTCTTTG[T/C]
TGCTCCTCCAACATGTCCTTAACTTTTGTGGGCCACTTCTTTCCACTCAGGATATCTACAGTTGCCTCTTTGTGTCTATCGACAAACCAACTATTGCACT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	36.90%	0.10%	2.54%	60.43%	NA
All Indica	2759	5.40%	0.10%	2.68%	91.77%	NA
All Japonica	1512	95.70%	0.00%	0.00%	4.30%	NA
Aus	269	4.10%	0.70%	13.01%	82.16%	NA
Indica I	595	7.40%	0.20%	2.02%	90.42%	NA
Indica II	465	5.80%	0.20%	0.86%	93.12%	NA
Indica III	913	2.50%	0.00%	3.18%	94.30%	NA
Indica Intermediate	786	7.10%	0.10%	3.69%	89.06%	NA
Temperate Japonica	767	99.20%	0.00%	0.00%	0.78%	NA
Tropical Japonica	504	88.70%	0.00%	0.00%	11.31%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	89.60%	0.00%	8.33%	2.08%	NA
Intermediate	90	56.70%	0.00%	3.33%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1023134528	A -> G	LOC_Os10g42910.1	synonymous_variant ; p.Gln677Gln; LOW	synonymous_codon	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg1023134528	A -> DEL	LOC_Os10g42910.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1023134528	4.64E-07	1.62E-06	mr1588	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
vg1023134528	NA	2.62E-12	mr1713	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
vg1023134528	NA	9.70E-06	mr1348_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