Search for Variation information by Variation ID:

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

Detailed information for vg0709674724:

Variant ID: vg0709674724 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9674724
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GATTATCTTAACCCCTGCTTATAATTTATATATCACAAGTAATATATAAATTATTAGTTGAGTTCTCTCTACATGATCTTCCCACGGGATAAAATAAATA[C/T]
GATACCCTTGGAATACTTTCGGGTGAAATGTTCCAATGGTATATCCGTGCACTTGCGGATAAACTCCGTAACCATAATATACCAGAAGTATTTCTGCGCC

Reverse complement sequence

GGCGCAGAAATACTTCTGGTATATTATGGTTACGGAGTTTATCCGCAAGTGCACGGATATACCATTGGAACATTTCACCCGAAAGTATTCCAAGGGTATC[G/A]
TATTTATTTTATCCCGTGGGAAGATCATGTAGAGAGAACTCAACTAATAATTTATATATTACTTGTGATATATAAATTATAAGCAGGGGTTAAGATAATC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.90%	41.40%	1.31%	5.37%	NA
All Indica	2759	82.80%	12.80%	0.87%	3.59%	NA
All Japonica	1512	1.70%	87.00%	2.31%	8.99%	NA
Aus	269	32.00%	66.20%	0.37%	1.49%	NA
Indica I	595	65.90%	25.90%	2.18%	6.05%	NA
Indica II	465	90.80%	5.80%	1.08%	2.37%	NA
Indica III	913	96.40%	1.60%	0.00%	1.97%	NA
Indica Intermediate	786	75.10%	19.80%	0.76%	4.33%	NA
Temperate Japonica	767	2.10%	86.70%	0.39%	10.82%	NA
Tropical Japonica	504	1.00%	88.30%	5.16%	5.56%	NA
Japonica Intermediate	241	2.10%	85.10%	2.49%	10.37%	NA
VI/Aromatic	96	16.70%	71.90%	1.04%	10.42%	NA
Intermediate	90	46.70%	46.70%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0709674724	C -> DEL	N	N	silent_mutation	Average:28.49; most accessible tissue: Zhenshan97 flag leaf, score: 40.929	N	N	N	N
vg0709674724	C -> T	LOC_Os07g16510.1	downstream_gene_variant ; 1401.0bp to feature; MODIFIER	silent_mutation	Average:28.49; most accessible tissue: Zhenshan97 flag leaf, score: 40.929	N	N	N	N
vg0709674724	C -> T	LOC_Os07g16500.1	intron_variant ; MODIFIER	silent_mutation	Average:28.49; most accessible tissue: Zhenshan97 flag leaf, score: 40.929	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709674724	NA	2.94E-07	mr1026	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
vg0709674724	NA	3.62E-06	mr1063	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
vg0709674724	NA	2.42E-06	mr1161	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
vg0709674724	NA	2.33E-16	mr1260_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
vg0709674724	NA	1.75E-06	mr1442_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
vg0709674724	4.60E-06	NA	mr1510_2	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
vg0709674724	NA	5.69E-13	mr1521_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
vg0709674724	NA	4.30E-08	mr1533_2	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
vg0709674724	NA	1.21E-29	mr1580_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
vg0709674724	NA	8.00E-07	mr1624_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
vg0709674724	NA	6.05E-09	mr1751_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
vg0709674724	NA	4.11E-30	mr1825_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
vg0709674724	4.77E-06	8.55E-09	mr1980_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