RiceVarMap2

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Detailed information for vg0314622348:

Variant ID: vg0314622348 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14622348
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTATTCGAGATAATCCGTATTTGTTTCCGTATTCGAGGTATCCGTATTCGTTTTCGTATCTGGTAAAAAATATGAAAACGAATATGATACGAGCATTAT[C/T]
CGTCCGTATCCGCTCCATTTTCATCCCTATCGTACAGTGGTATTTTCTGAAAGTTACATCCGCCGATACATTTATTGGAACAGGGTGCTCGTCAATGGTA

Reverse complement sequence

TACCATTGACGAGCACCCTGTTCCAATAAATGTATCGGCGGATGTAACTTTCAGAAAATACCACTGTACGATAGGGATGAAAATGGAGCGGATACGGACG[G/A]
ATAATGCTCGTATCATATTCGTTTTCATATTTTTTACCAGATACGAAAACGAATACGGATACCTCGAATACGGAAACAAATACGGATTATCTCGAATACG

Allele Frequencies:

Search:

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	86.30%	11.50%	2.20%	0.00%	NA
All Indica	2759	99.90%	0.00%	0.11%	0.00%	NA
All Japonica	1512	57.90%	35.50%	6.61%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.00%	0.25%	0.00%	NA
Temperate Japonica	767	26.20%	62.60%	11.21%	0.00%	NA
Tropical Japonica	504	92.70%	6.30%	0.99%	0.00%	NA
Japonica Intermediate	241	85.90%	10.40%	3.73%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	1.11%	0.00%	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
vg0314622348	C -> T	LOC_Os03g25560-LOC_Os03g25570	intergenic_region ; MODIFIER	silent_mutation	Average:37.272; most accessible tissue: Zhenshan97 young leaf, score: 49.329	N	N	N	N

Showing 1 to 1 of 1 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314622348	NA	3.15E-13	Plant_height	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0314622348	NA	1.17E-16	Spikelet_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0314622348	NA	4.38E-13	Spikelet_length	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0314622348	NA	3.19E-08	mr1045	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
vg0314622348	NA	2.75E-07	mr1045	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
vg0314622348	NA	3.57E-25	mr1115	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
vg0314622348	NA	3.99E-32	mr1137	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
vg0314622348	NA	2.29E-10	mr1137	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
vg0314622348	NA	5.44E-08	mr1162	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
vg0314622348	NA	5.90E-06	mr1164	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

Showing 1 to 10 of 69 entries

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Search for Variation information by Variation ID:

Detailed information for vg0314622348:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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