RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg1006612280:

Variant ID: vg1006612280 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 6612280
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, T: 0.07, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

CAATACTTTTGACAAGATCATGAACTCCCAATGTCCGCATCATCCAAATTCCAATCATGCGGCCAAAGATTGCTTCGTCTACAAACAGTTTGCAGAACAA[A/T]
ACACCAAGAATGCACGAAAGGCCTCCGACGGAGATCAAAGCATGTCAAAAAAGAAGGACGATGACGACGATGCCCCGATAGGTTTTCGAGACCGTCGTAA

Reverse complement sequence

TTACGACGGTCTCGAAAACCTATCGGGGCATCGTCGTCATCGTCCTTCTTTTTTGACATGCTTTGATCTCCGTCGGAGGCCTTTCGTGCATTCTTGGTGT[T/A]
TTGTTCTGCAAACTGTTTGTAGACGAAGCAATCTTTGGCCGCATGATTGGAATTTGGATGATGCGGACATTGGGAGTTCATGATCTTGTCAAAAGTATTG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	22.20%	19.60%	1.33%	56.83%	NA
All Indica	2759	36.50%	1.60%	1.74%	60.17%	NA
All Japonica	1512	0.90%	56.70%	0.20%	42.20%	NA
Aus	269	2.20%	0.40%	4.09%	93.31%	NA
Indica I	595	10.10%	2.00%	4.37%	83.53%	NA
Indica II	465	60.60%	1.10%	0.43%	37.85%	NA
Indica III	913	36.80%	1.20%	0.55%	61.45%	NA
Indica Intermediate	786	41.90%	2.00%	1.91%	54.20%	NA
Temperate Japonica	767	0.40%	88.90%	0.00%	10.69%	NA
Tropical Japonica	504	0.40%	8.70%	0.40%	90.48%	NA
Japonica Intermediate	241	3.30%	54.80%	0.41%	41.49%	NA
VI/Aromatic	96	3.10%	5.20%	1.04%	90.62%	NA
Intermediate	90	24.40%	20.00%	0.00%	55.56%	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
vg1006612280	A -> T	LOC_Os10g11920.1	missense_variant ; p.Asn28Tyr; MODERATE	nonsynonymous_codon	Average:9.839; most accessible tissue: Callus, score: 25.028	probably damaging	-2.157	TOLERATED	1.00
vg1006612280	A -> DEL	LOC_Os10g11920.1	N	frameshift_variant	Average:9.839; most accessible tissue: Callus, score: 25.028	N	N	N	N

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
vg1006612280	7.48E-06	NA	mr1217	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
vg1006612280	3.40E-06	2.03E-06	mr1345	Jap_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
vg1006612280	3.66E-06	3.14E-06	mr1401	Jap_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
vg1006612280	2.84E-07	2.84E-07	mr1417	Jap_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
vg1006612280	5.81E-06	NA	mr1515	Jap_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
vg1006612280	4.10E-06	NA	mr1611	Jap_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
vg1006612280	1.86E-06	1.86E-06	mr1635	Jap_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
vg1006612280	9.30E-06	NA	mr1816	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
vg1006612280	1.77E-06	1.77E-06	mr1823	Jap_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
vg1006612280	1.26E-06	NA	mr1844	Jap_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 10 of 11 entries

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Search for Variation information by Variation ID:

Detailed information for vg1006612280:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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