RiceVarMap2

Detailed information for vg0713015396:

Variant ID: vg0713015396 (JBrowse)

Variation Type: SNP

Chromosome: chr07

Position: 13015396

Reference Allele: A

Alternative Allele: T

Primary Allele: A

Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, T: 0.04, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

GCTCATCACCTTTCTTCAAAATAATAAAGATATCTTTGCGTGGAAACCATCTGATATGCCAGGTATTCCCAGAGAGGTGATTGAGCACTCTTTACATGTT[A/T]
AGGAAGACGCTAAACCTATCAAGCAACAACTCCACCGTTTCGCACAGGATAGGAAGGATGCGATCAAGGAAGAATTGACTAAGCTGTTAGCAGCGGGCTT

Reverse complement sequence

AAGCCCGCTGCTAACAGCTTAGTCAATTCTTCCTTGATCGCATCCTTCCTATCCTGTGCGAAACGGTGGAGTTGTTGCTTGATAGGTTTAGCGTCTTCCT[T/A]
AACATGTAAAGAGTGCTCAATCACCTCTCTGGGAATACCTGGCATATCAGATGGTTTCCACGCAAAGATATCTTTATTATTTTGAAGAAAGGTGATGAGC

Allele Frequencies:

Search:

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	31.10%	7.20%	2.94%	58.76%	NA
All Indica	2759	6.20%	12.10%	3.15%	78.62%	NA
All Japonica	1512	79.10%	0.10%	1.46%	19.31%	NA
Aus	269	21.60%	0.00%	4.46%	73.98%	NA
Indica I	595	6.20%	32.80%	2.69%	58.32%	NA
Indica II	465	9.20%	6.00%	3.23%	81.51%	NA
Indica III	913	2.50%	0.40%	3.72%	93.32%	NA
Indica Intermediate	786	8.50%	13.50%	2.80%	75.19%	NA
Temperate Japonica	767	73.30%	0.10%	1.17%	25.42%	NA
Tropical Japonica	504	86.90%	0.00%	1.19%	11.90%	NA
Japonica Intermediate	241	81.30%	0.40%	2.90%	15.35%	NA
VI/Aromatic	96	7.30%	1.00%	16.67%	75.00%	NA
Intermediate	90	44.40%	3.30%	2.22%	50.00%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0713015396	A -> DEL	LOC_Os07g23070.1	N	frameshift_variant	Average:11.559; most accessible tissue: Callus, score: 21.234	N	N	N	N
vg0713015396	A -> T	LOC_Os07g23070.1	stop_gained ; p.Lys742*; HIGH	stop_gained	Average:11.559; most accessible tissue: Callus, score: 21.234	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

Show entries

Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713015396	8.44E-06	9.46E-07	mr1063	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
vg0713015396	NA	1.26E-07	mr1527	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
vg0713015396	NA	5.32E-13	mr1744	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

Showing 1 to 3 of 3 entries

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Detailed information for vg0713015396:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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