RiceVarMap2

Detailed information for vg0324116929:

Variant ID: vg0324116929 (JBrowse)

Variation Type: SNP

Chromosome: chr03

Position: 24116929

Reference Allele: A

Alternative Allele: G

Primary Allele: A

Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGATTTTGGAGAAGTTCTCGATGAACCTCCGGTAGTATCCTGCCAAACCCAAAAAGCTGCGAACCTGAGTAACTATCTTGGGTTGCTTCCAATCAGTGAC[A/G]
GCGGTTACTGTTTCGGGGTCCACAGCAACTCCTTTAGTGGATATCACGTGCCCTAAGAACTTGACTTCGGACAACCAGAACTCACACTTGCTGAGCTTGC

Reverse complement sequence

GCAAGCTCAGCAAGTGTGAGTTCTGGTTGTCCGAAGTCAAGTTCTTAGGGCACGTGATATCCACTAAAGGAGTTGCTGTGGACCCCGAAACAGTAACCGC[T/C]
GTCACTGATTGGAAGCAACCCAAGATAGTTACTCAGGTTCGCAGCTTTTTGGGTTTGGCAGGATACTACCGGAGGTTCATCGAGAACTTCTCCAAAATCG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	41.20%	25.10%	12.17%	21.50%	NA
All Indica	2759	7.90%	36.60%	20.08%	35.45%	NA
All Japonica	1512	99.30%	0.10%	0.13%	0.46%	NA
Aus	269	40.50%	55.00%	1.12%	3.35%	NA
Indica I	595	10.80%	13.10%	23.87%	52.27%	NA
Indica II	465	7.50%	20.90%	30.97%	40.65%	NA
Indica III	913	2.60%	61.70%	11.39%	24.32%	NA
Indica Intermediate	786	12.00%	34.60%	20.87%	32.57%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	99.20%	0.00%	0.20%	0.60%	NA
Japonica Intermediate	241	98.30%	0.80%	0.41%	0.41%	NA
VI/Aromatic	96	76.00%	14.60%	7.29%	2.08%	NA
Intermediate	90	52.20%	15.60%	10.00%	22.22%	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
vg0324116929	A -> DEL	LOC_Os03g43250.1	N	frameshift_variant	Average:11.677; most accessible tissue: Callus, score: 30.379	N	N	N	N
vg0324116929	A -> G	LOC_Os03g43250.1	synonymous_variant ; p.Ala429Ala; LOW	synonymous_codon	Average:11.677; most accessible tissue: Callus, score: 30.379	N	N	N	N

Showing 1 to 2 of 2 entries

Putative Genotype-Phenotype Associations:

Show entries

Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0324116929	NA	4.13E-12	mr1744	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
vg0324116929	4.14E-06	4.14E-06	mr1187_2	Ind_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 2 of 2 entries

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Detailed information for vg0324116929:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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