RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0719650559:

Variant ID: vg0719650559 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 19650559
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TACAAGCTTCTGCACCTACTGCTACTACTGATCACAATGCCAACAAGGCCTCGGAGTTGGCACGCAGCTGCTCCTTCTCCAGCACAAACATCTTCAGCCG[C/A]
GGCAGCGACTTGCCGGCCGTGTTCGGCCGCGGGGCCGCCATGTTTGCCGGGGTCGGGGTCGGGGCCGGGCGCGGCGCGGGCAGCTTGACGTCCTTGACGG

Reverse complement sequence

CCGTCAAGGACGTCAAGCTGCCCGCGCCGCGCCCGGCCCCGACCCCGACCCCGGCAAACATGGCGGCCCCGCGGCCGAACACGGCCGGCAAGTCGCTGCC[G/T]
CGGCTGAAGATGTTTGTGCTGGAGAAGGAGCAGCTGCGTGCCAACTCCGAGGCCTTGTTGGCATTGTGATCAGTAGTAGCAGTAGGTGCAGAAGCTTGTA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.40%	6.60%	0.95%	8.06%	NA
All Indica	2759	96.90%	0.10%	0.87%	2.14%	NA
All Japonica	1512	78.80%	20.20%	0.13%	0.79%	NA
Aus	269	9.30%	0.00%	5.58%	85.13%	NA
Indica I	595	99.80%	0.00%	0.00%	0.17%	NA
Indica II	465	93.10%	0.00%	3.23%	3.66%	NA
Indica III	913	98.80%	0.00%	0.00%	1.20%	NA
Indica Intermediate	786	94.80%	0.30%	1.15%	3.82%	NA
Temperate Japonica	767	59.80%	39.20%	0.26%	0.65%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	95.40%	1.70%	0.00%	2.90%	NA
VI/Aromatic	96	20.80%	0.00%	2.08%	77.08%	NA
Intermediate	90	86.70%	3.30%	2.22%	7.78%	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
vg0719650559	C -> DEL	LOC_Os07g32850.1	N	frameshift_variant	Average:43.104; most accessible tissue: Zhenshan97 root, score: 72.671	N	N	N	N
vg0719650559	C -> A	LOC_Os07g32850.1	synonymous_variant ; p.Pro140Pro; LOW	nonsynonymous_codon ; P140H	Average:43.104; most accessible tissue: Zhenshan97 root, score: 72.671	probably damaging	2.753	DELETERIOUS	0.01

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0719650559	9.25E-06	NA	Heading_date	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
vg0719650559	4.43E-06	NA	Plant_height	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
vg0719650559	1.53E-07	NA	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
vg0719650559	1.20E-06	NA	Spikelet_length	Jap_All	YES	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

Showing 1 to 4 of 4 entries

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Search for Variation information by Variation ID:

Detailed information for vg0719650559:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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