RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0221575685:

Variant ID: vg0221575685 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21575685
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGCACGAACTCGAGGAGGAATACTACCCTGTTGTCGACTACGAGTCAGACCTTCAGACCGCCATGTCGACAACAGTTAAATAGGCTACCCCAAGGCTAC[T/C]
CCAAATATTGTACTGGTGTGATTATGGTGAATAAGAGCAATATCGGCTTCGGCCAACAGGATGTAGGGTTATTACCTAACAATTCAGGGGCCTGAACCTG

Reverse complement sequence

CAGGTTCAGGCCCCTGAATTGTTAGGTAATAACCCTACATCCTGTTGGCCGAAGCCGATATTGCTCTTATTCACCATAATCACACCAGTACAATATTTGG[A/G]
GTAGCCTTGGGGTAGCCTATTTAACTGTTGTCGACATGGCGGTCTGAAGGTCTGACTCGTAGTCGACAACAGGGTAGTATTCCTCCTCGAGTTCGTGCCC

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	64.90%	35.00%	0.08%	0.00%	NA
All Indica	2759	97.70%	2.20%	0.04%	0.00%	NA
All Japonica	1512	3.60%	96.40%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	98.30%	1.50%	0.17%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	98.20%	1.80%	0.00%	0.00%	NA
Indica Intermediate	786	95.90%	4.10%	0.00%	0.00%	NA
Temperate Japonica	767	1.40%	98.60%	0.00%	0.00%	NA
Tropical Japonica	504	7.30%	92.70%	0.00%	0.00%	NA
Japonica Intermediate	241	2.90%	97.10%	0.00%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	40.00%	56.70%	3.33%	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
vg0221575685	T -> C	LOC_Os02g35910.1	upstream_gene_variant ; 1478.0bp to feature; MODIFIER	silent_mutation	Average:78.329; most accessible tissue: Zhenshan97 flag leaf, score: 94.34	N	N	N	N
vg0221575685	T -> C	LOC_Os02g35920.1	upstream_gene_variant ; 4969.0bp to feature; MODIFIER	silent_mutation	Average:78.329; most accessible tissue: Zhenshan97 flag leaf, score: 94.34	N	N	N	N
vg0221575685	T -> C	LOC_Os02g35910-LOC_Os02g35920	intergenic_region ; MODIFIER	silent_mutation	Average:78.329; most accessible tissue: Zhenshan97 flag leaf, score: 94.34	N	N	N	N

Showing 1 to 3 of 3 entries

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

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Search:

Var ID	Ref	Alt	Root (RT)	Young Leaf (YL)	Flag Leaf (FL)	Young Panicle (YP)	Lemma & Palea (LP)	Stamen & Pistil (SP)
vg0221575685	T	C	-0.03	-0.05	-0.03	0.01	-0.02	-0.02

Showing 1 to 1 of 1 entries

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Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221575685	NA	9.96E-71	mr1014	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
vg0221575685	NA	2.16E-26	mr1024	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
vg0221575685	NA	6.30E-12	mr1128	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
vg0221575685	NA	5.95E-80	mr1134	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
vg0221575685	NA	5.02E-74	mr1135	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
vg0221575685	NA	2.28E-44	mr1194	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
vg0221575685	NA	1.63E-12	mr1205	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
vg0221575685	NA	8.51E-26	mr1375	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
vg0221575685	NA	1.68E-08	mr1442	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
vg0221575685	NA	1.66E-87	mr1504	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 vg0221575685:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Effects Predicted by Deep Convolutional Neural Networks

Putative Genotype-Phenotype Associations:

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