Search for Variation information by Variation ID:

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

Detailed information for vg1120445414:

Variant ID: vg1120445414 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 20445414
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTGTTCGAAGATTCTGCATGGCTCCTTGTGCAAACTCGATCTCCATGGTGTCACTCCAGTACTCGAAAAGTGATAGGCACTTGAATCGGTAGCTGATTA[T/A]
CAGCCTCTCATCCCTGTCCACTGTGGGTTTCTCCACTCCTAGATAGAGACGACTAAGAGATGGTATGCTCCCAAGTATTTGCAGGTCCCTCTCTTTCAGT

Reverse complement sequence

ACTGAAAGAGAGGGACCTGCAAATACTTGGGAGCATACCATCTCTTAGTCGTCTCTATCTAGGAGTGGAGAAACCCACAGTGGACAGGGATGAGAGGCTG[A/T]
TAATCAGCTACCGATTCAAGTGCCTATCACTTTTCGAGTACTGGAGTGACACCATGGAGATCGAGTTTGCACAAGGAGCCATGCAGAATCTTCGAACACT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.10%	27.70%	0.55%	22.68%	NA
All Indica	2759	63.40%	5.50%	0.62%	30.48%	NA
All Japonica	1512	34.10%	60.40%	0.00%	5.49%	NA
Aus	269	3.30%	49.80%	2.23%	44.61%	NA
Indica I	595	49.60%	1.20%	1.34%	47.90%	NA
Indica II	465	75.90%	1.90%	0.22%	21.94%	NA
Indica III	913	61.10%	8.10%	0.44%	30.34%	NA
Indica Intermediate	786	69.20%	7.80%	0.51%	22.52%	NA
Temperate Japonica	767	16.80%	79.30%	0.00%	3.91%	NA
Tropical Japonica	504	44.80%	45.40%	0.00%	9.72%	NA
Japonica Intermediate	241	66.40%	32.00%	0.00%	1.66%	NA
VI/Aromatic	96	3.10%	74.00%	2.08%	20.83%	NA
Intermediate	90	46.70%	43.30%	1.11%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1120445414	T -> A	LOC_Os11g34880.1	missense_variant ; p.Ile492Leu; MODERATE	nonsynonymous_codon ; I492L	Average:43.889; most accessible tissue: Callus, score: 85.408	unknown	unknown	TOLERATED	0.30
vg1120445414	T -> DEL	LOC_Os11g34880.1	N	frameshift_variant	Average:43.889; most accessible tissue: Callus, score: 85.408	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120445414	NA	2.66E-07	mr1126_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