RiceVarMap2

Detailed information for vg0403594374:

Variant ID: vg0403594374 (JBrowse)

Variation Type: SNP

Chromosome: chr04

Position: 3594374

Reference Allele: A

Alternative Allele: G

Primary Allele: G

Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.12, others allele: 0.00, population size: 57. )

Flanking Sequence (100 bp) in Reference Genome:

GCGAAACACCCCCAACCTCGTCTAGTCCCTAGGCGAAGATGTCGATGTTTTTCTTGAGCACAGCCAACATGTTGTTCGTTTCTTCTTCACTTAGATCGCC[A/G]
CCTAGGGAAACCACCTTGGTTTGTTCATCCTCATCAACTTGGACCTTGATCACCTTGCCATGCGGAGATGACTTCGGCATGACTCTTGCTTGTTCACCTT

Reverse complement sequence

AAGGTGAACAAGCAAGAGTCATGCCGAAGTCATCTCCGCATGGCAAGGTGATCAAGGTCCAAGTTGATGAGGATGAACAAACCAAGGTGGTTTCCCTAGG[T/C]
GGCGATCTAAGTGAAGAAGAAACGAACAACATGTTGGCTGTGCTCAAGAAAAACATCGACATCTTCGCCTAGGGACTAGACGAGGTTGGGGGTGTTTCGC

Allele Frequencies:

Search:

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	32.50%	19.00%	0.74%	47.80%	NA
All Indica	2759	51.40%	2.20%	0.91%	45.49%	NA
All Japonica	1512	4.80%	52.60%	0.20%	42.39%	NA
Aus	269	1.90%	3.30%	2.23%	92.57%	NA
Indica I	595	96.10%	0.50%	0.17%	3.19%	NA
Indica II	465	50.80%	4.70%	1.29%	43.23%	NA
Indica III	913	24.90%	1.00%	1.10%	73.06%	NA
Indica Intermediate	786	48.70%	3.40%	1.02%	46.82%	NA
Temperate Japonica	767	7.80%	47.20%	0.26%	44.72%	NA
Tropical Japonica	504	0.60%	68.80%	0.20%	30.36%	NA
Japonica Intermediate	241	3.70%	36.10%	0.00%	60.17%	NA
VI/Aromatic	96	4.20%	7.30%	1.04%	87.50%	NA
Intermediate	90	38.90%	27.80%	0.00%	33.33%	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
vg0403594374	A -> DEL	N	N	silent_mutation	Average:31.101; most accessible tissue: Zhenshan97 flag leaf, score: 71.238	N	N	N	N
vg0403594374	A -> G	LOC_Os04g06820.1	intron_variant ; MODIFIER	silent_mutation	Average:31.101; most accessible tissue: Zhenshan97 flag leaf, score: 71.238	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
vg0403594374	2.22E-06	9.92E-07	mr1588	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
vg0403594374	NA	1.27E-06	mr1727_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

Showing 1 to 2 of 2 entries

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Search for Variation information by Variation ID:

Detailed information for vg0403594374:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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