Search for Variation information by Variation ID:

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

Detailed information for vg0622436576:

Variant ID: vg0622436576 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22436576
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

CATCATAGGGTAGTCAACCTCTGGTTGCTCCTCGTACTGTGACTCCTCGTACGCGTGCTGGTCCACCTTAGGGCGGCCGATCGCAATCCTCTCAGCTGCC[C/T]
AGATAGAAAGAAAGAGAGGGCACCCACCAAAGGTCGCGCTGGGATCCGTCTTCGTGCAAGACTCACAAAGTGCACGGTACAGAGCCACCAATAATGCGGA

Reverse complement sequence

TCCGCATTATTGGTGGCTCTGTACCGTGCACTTTGTGAGTCTTGCACGAAGACGGATCCCAGCGCGACCTTTGGTGGGTGCCCTCTCTTTCTTTCTATCT[G/A]
GGCAGCTGAGAGGATTGCGATCGGCCGCCCTAAGGTGGACCAGCACGCGTACGAGGAGTCACAGTACGAGGAGCAACCAGAGGTTGACTACCCTATGATG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.60%	16.10%	2.60%	35.72%	NA
All Indica	2759	37.40%	2.00%	4.17%	56.43%	NA
All Japonica	1512	57.50%	39.90%	0.07%	2.51%	NA
Aus	269	64.30%	10.80%	1.12%	23.79%	NA
Indica I	595	17.00%	0.70%	4.37%	77.98%	NA
Indica II	465	29.50%	1.90%	3.87%	64.73%	NA
Indica III	913	56.20%	2.80%	4.05%	36.91%	NA
Indica Intermediate	786	35.60%	2.20%	4.33%	57.89%	NA
Temperate Japonica	767	68.40%	30.20%	0.00%	1.30%	NA
Tropical Japonica	504	52.80%	42.50%	0.20%	4.56%	NA
Japonica Intermediate	241	32.40%	65.60%	0.00%	2.07%	NA
VI/Aromatic	96	45.80%	50.00%	0.00%	4.17%	NA
Intermediate	90	43.30%	24.40%	4.44%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0622436576	C -> T	LOC_Os06g37890.1	N	stop_gained	Average:29.115; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0622436576	C -> DEL	LOC_Os06g37890.1	N	frameshift_variant	Average:29.115; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622436576	2.86E-06	NA	mr1183_2	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