RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0528104538:

Variant ID: vg0528104538 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 28104538
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAAAGTTTGGTTTGAAAATACAATTCCTTGCAAGCTGCAGGGCTGTTGGATGCTGGGTTGCTGCAGGGAGGGGCGGCGCCGCCGCCGCCCTCGGCGACG[G/A]
TGGTGGCGGTGAGCCGCGACGACGAGACGATGTGCACCAAGACCACGAGCTACAGCTTCCCGGCGACGATGCACCTCAACGTGAAGATGTTCGGCGAGGC

Reverse complement sequence

GCCTCGCCGAACATCTTCACGTTGAGGTGCATCGTCGCCGGGAAGCTGTAGCTCGTGGTCTTGGTGCACATCGTCTCGTCGTCGCGGCTCACCGCCACCA[C/T]
CGTCGCCGAGGGCGGCGGCGGCGCCGCCCCTCCCTGCAGCAACCCAGCATCCAACAGCCCTGCAGCTTGCAAGGAATTGTATTTTCAAACCAAACTTTAA

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	93.60%	6.10%	0.32%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	80.20%	18.80%	0.99%	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	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	67.00%	31.20%	1.83%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	82.20%	17.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0528104538	G -> A	LOC_Os05g48990.1	missense_variant ; p.Val443Met; MODERATE	nonsynonymous_codon ; V443M	Average:53.147; most accessible tissue: Minghui63 panicle, score: 70.194	unknown	unknown	TOLERATED	0.12

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
vg0528104538	NA	1.09E-13	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
vg0528104538	NA	2.34E-10	Heading_date	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
vg0528104538	NA	1.90E-14	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
vg0528104538	NA	5.43E-06	mr1092	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
vg0528104538	NA	2.98E-07	mr1252	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
vg0528104538	6.28E-07	NA	mr1300	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
vg0528104538	3.78E-09	NA	mr1310	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
vg0528104538	1.98E-10	NA	mr1926	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
vg0528104538	NA	1.14E-06	mr1097_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
vg0528104538	NA	2.94E-06	mr1129_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

Showing 1 to 10 of 18 entries

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Search for Variation information by Variation ID:

Detailed information for vg0528104538:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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