RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0709436324:

Variant ID: vg0709436324 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9436324
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.08, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

ATCGGTTAGATCGCCGGTTTGCTCGTTACGGAACCCCAACTTATCATTTGTGTTCCATTCCTATTTGCAATTCAGATTGCTTTTATCTTGTTCTTACTTG[A/G]
CAGTTGAGCTCATTGGTCCACATACATCAGTATGTACTAGTGCCAATAGTTCACTTGCCCTTTCACTTTGACCCGTGAAAGGTGCCTTTGTCATCTTGCC

Reverse complement sequence

GGCAAGATGACAAAGGCACCTTTCACGGGTCAAAGTGAAAGGGCAAGTGAACTATTGGCACTAGTACATACTGATGTATGTGGACCAATGAGCTCAACTG[T/C]
CAAGTAAGAACAAGATAAAAGCAATCTGAATTGCAAATAGGAATGGAACACAAATGATAAGTTGGGGTTCCGTAACGAGCAAACCGGCGATCTAACCGAT

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	68.10%	30.50%	0.11%	1.25%	NA
All Indica	2759	98.30%	1.60%	0.00%	0.11%	NA
All Japonica	1512	17.20%	78.80%	0.33%	3.70%	NA
Aus	269	40.10%	59.90%	0.00%	0.00%	NA
Indica I	595	99.20%	0.50%	0.00%	0.34%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	96.90%	2.90%	0.00%	0.13%	NA
Temperate Japonica	767	12.10%	79.90%	0.65%	7.30%	NA
Tropical Japonica	504	16.70%	83.30%	0.00%	0.00%	NA
Japonica Intermediate	241	34.40%	65.60%	0.00%	0.00%	NA
VI/Aromatic	96	81.20%	18.80%	0.00%	0.00%	NA
Intermediate	90	68.90%	31.10%	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
vg0709436324	A -> DEL	LOC_Os07g16190.1	N	frameshift_variant	Average:27.674; most accessible tissue: Minghui63 flag leaf, score: 38.911	N	N	N	N
vg0709436324	A -> G	LOC_Os07g16190.1	missense_variant ; p.Val376Ala; MODERATE	nonsynonymous_codon ; V376A	Average:27.674; most accessible tissue: Minghui63 flag leaf, score: 38.911	unknown	unknown	TOLERATED	1.00

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
vg0709436324	NA	1.70E-06	mr1028	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
vg0709436324	NA	9.09E-23	mr1051	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
vg0709436324	NA	1.87E-06	mr1058	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
vg0709436324	5.32E-06	NA	mr1117	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
vg0709436324	NA	4.48E-21	mr1131	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
vg0709436324	NA	4.42E-17	mr1147	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
vg0709436324	NA	1.34E-18	mr1179	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
vg0709436324	NA	4.47E-11	mr1195	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
vg0709436324	6.77E-06	NA	mr1247	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
vg0709436324	NA	1.33E-07	mr1280	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 52 entries

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Search for Variation information by Variation ID:

Detailed information for vg0709436324:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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