Search for Variation information by Variation ID:

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

Detailed information for vg0708118551:

Variant ID: vg0708118551 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 8118551
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTCACCTTGACCAACGAGAAGGGAGAAACCGTAGTGTACAAATCACTAGTCTCACCAAAGCAAGGGGTCTCCTTGAATCAGATTGAGGCGGAAATCCCA[G/A]
TGGTCACGAAGGAGAAGAATCCGAGGAAATTGGAAGAGATTCCCATAGTTTGCGAGTACCCAGAAGTCTTTCCTGAAGACCTCACTACCATGCCACCCAA

Reverse complement sequence

TTGGGTGGCATGGTAGTGAGGTCTTCAGGAAAGACTTCTGGGTACTCGCAAACTATGGGAATCTCTTCCAATTTCCTCGGATTCTTCTCCTTCGTGACCA[C/T]
TGGGATTTCCGCCTCAATCTGATTCAAGGAGACCCCTTGCTTTGGTGAGACTAGTGATTTGTACACTACGGTTTCTCCCTTCTCGTTGGTCAAGGTGACT

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	27.90%	7.00%	33.05%	32.08%	NA
All Indica	2759	2.10%	0.30%	50.82%	46.79%	NA
All Japonica	1512	66.10%	20.60%	1.98%	11.24%	NA
Aus	269	57.20%	0.00%	34.94%	7.81%	NA
Indica I	595	0.70%	0.20%	16.30%	82.86%	NA
Indica II	465	4.10%	1.30%	53.12%	41.51%	NA
Indica III	913	1.10%	0.00%	71.41%	27.49%	NA
Indica Intermediate	786	3.20%	0.10%	51.65%	45.04%	NA
Temperate Japonica	767	84.40%	0.50%	1.04%	14.08%	NA
Tropical Japonica	504	25.80%	59.90%	3.97%	10.32%	NA
Japonica Intermediate	241	92.50%	2.50%	0.83%	4.15%	NA
VI/Aromatic	96	78.10%	0.00%	11.46%	10.42%	NA
Intermediate	90	35.60%	10.00%	27.78%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0708118551	G -> DEL	LOC_Os07g14250.1	N	frameshift_variant	Average:8.734; most accessible tissue: Callus, score: 23.913	N	N	N	N
vg0708118551	G -> A	LOC_Os07g14250.1	missense_variant ; p.Val536Met; MODERATE	nonsynonymous_codon ; V536M	Average:8.734; most accessible tissue: Callus, score: 23.913	probably damaging	2.247	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0708118551	2.63E-06	NA	mr1076	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
vg0708118551	NA	8.01E-06	mr1082	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
vg0708118551	4.63E-06	NA	mr1226	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
vg0708118551	NA	2.07E-08	mr1408	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
vg0708118551	4.17E-07	NA	mr1082_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
vg0708118551	9.79E-06	NA	mr1083_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
vg0708118551	3.51E-06	NA	mr1104_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
vg0708118551	1.28E-06	NA	mr1107_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
vg0708118551	1.11E-06	NA	mr1226_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
vg0708118551	NA	1.58E-07	mr1363_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
vg0708118551	NA	8.45E-08	mr1363_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
vg0708118551	NA	1.14E-09	mr1408_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
vg0708118551	NA	3.33E-08	mr1798_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
vg0708118551	1.58E-06	2.22E-11	mr1800_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
vg0708118551	NA	1.50E-08	mr1862_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