RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg1211633613:

Variant ID: vg1211633613 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 11633613
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

TACCCCCAACTGATTTCTCCCCACGAATGGCACAGATATAAACGAGTGGGAAGCTCCAGAGTCGAACAAAATGGTAGCAGGGATGGAATGTATGAGGAAC[G/A]
TACCAACGATGACGTCTGGAGTTGTCAGCACGCCCTCGGCCGTCACGTGGTTCACACGGCCCCGAATGACATCCTTACCACCATTGTTGGAGCGGGGAGG

Reverse complement sequence

CCTCCCCGCTCCAACAATGGTGGTAAGGATGTCATTCGGGGCCGTGTGAACCACGTGACGGCCGAGGGCGTGCTGACAACTCCAGACGTCATCGTTGGTA[C/T]
GTTCCTCATACATTCCATCCCTGCTACCATTTTGTTCGACTCTGGAGCTTCCCACTCGTTTATATCTGTGCCATTCGTGGGGAGAAATCAGTTGGGGGTA

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	85.90%	4.60%	3.39%	6.12%	NA
All Indica	2759	95.00%	2.30%	1.63%	1.05%	NA
All Japonica	1512	80.20%	0.30%	2.58%	17.00%	NA
Aus	269	30.90%	43.90%	25.28%	0.00%	NA
Indica I	595	95.60%	1.00%	0.17%	3.19%	NA
Indica II	465	96.10%	1.10%	2.37%	0.43%	NA
Indica III	913	95.60%	2.60%	1.75%	0.00%	NA
Indica Intermediate	786	93.30%	3.60%	2.16%	1.02%	NA
Temperate Japonica	767	95.30%	0.00%	1.17%	3.52%	NA
Tropical Japonica	504	67.70%	0.40%	3.77%	28.17%	NA
Japonica Intermediate	241	58.10%	0.80%	4.56%	36.51%	NA
VI/Aromatic	96	67.70%	27.10%	4.17%	1.04%	NA
Intermediate	90	84.40%	8.90%	4.44%	2.22%	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
vg1211633613	G -> DEL	LOC_Os12g19980.1	N	frameshift_variant	Average:32.82; most accessible tissue: Zhenshan97 flag leaf, score: 63.67	N	N	N	N
vg1211633613	G -> A	LOC_Os12g19980.1	missense_variant ; p.Thr716Met; MODERATE	nonsynonymous_codon ; T716M	Average:32.82; most accessible tissue: Zhenshan97 flag leaf, score: 63.67	benign	0.762	DELETERIOUS	0.01

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1211633613	1.87E-06	2.96E-10	mr1016	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
vg1211633613	2.01E-07	4.85E-11	mr1019	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
vg1211633613	1.46E-06	NA	mr1055	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
vg1211633613	1.89E-08	NA	mr1055_2	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
vg1211633613	1.13E-06	NA	mr1132_2	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
vg1211633613	7.66E-08	NA	mr1390_2	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
vg1211633613	9.02E-09	NA	mr1490_2	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

Showing 1 to 7 of 7 entries

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Search for Variation information by Variation ID:

Detailed information for vg1211633613:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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