RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0106102408:

Variant ID: vg0106102408 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 6102408
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTACTCACGAAGTGGTTTTGGAGATGATTGGATTCACAGGTGATTTCATGTAACCGGTTAGACCGGGCTCTGGTAGCCGGTCAGACCGGCGTGTAATGC[G/A]
CGGTCAGACCGGCGCAGCCCGCGGTCTGACCGGCCGATACTGTGTCGGTTTCGGTTTCGGGTTGTTTGTTTGTATATCCGAGTTTATTTCTTGATTATGA

Reverse complement sequence

TCATAATCAAGAAATAAACTCGGATATACAAACAAACAACCCGAAACCGAAACCGACACAGTATCGGCCGGTCAGACCGCGGGCTGCGCCGGTCTGACCG[C/T]
GCATTACACGCCGGTCTGACCGGCTACCAGAGCCCGGTCTAACCGGTTACATGAAATCACCTGTGAATCCAATCATCTCCAAAACCACTTCGTGAGTAAA

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	96.80%	3.20%	0.00%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	90.30%	9.70%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	98.00%	2.00%	0.00%	0.00%	NA
Tropical Japonica	504	94.20%	5.80%	0.00%	0.00%	NA
Japonica Intermediate	241	57.30%	42.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	0.00%	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
vg0106102408	G -> A	LOC_Os01g11350-LOC_Os01g11360	intergenic_region ; MODIFIER	silent_mutation	Average:51.495; most accessible tissue: Minghui63 panicle, score: 73.225	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
vg0106102408	NA	6.29E-06	mr1114	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
vg0106102408	7.53E-06	2.47E-09	mr1117	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
vg0106102408	NA	9.50E-08	mr1118	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
vg0106102408	NA	1.31E-07	mr1119	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
vg0106102408	NA	1.94E-06	mr1120	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
vg0106102408	NA	5.03E-09	mr1123	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
vg0106102408	NA	1.81E-08	mr1180	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
vg0106102408	NA	6.31E-07	mr1183	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
vg0106102408	NA	5.85E-06	mr1240	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
vg0106102408	NA	3.58E-08	mr1242	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 32 entries

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Search for Variation information by Variation ID:

Detailed information for vg0106102408:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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