RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg1008769988:

Variant ID: vg1008769988 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 8769988
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.25, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

ATATCTTTGTGTTGTGGTAAGTCTTTTCTCTCCATTCCTCAAGTTCAGCGATCTGCATTTTTCTCCATTCTCCTGCTCCCTCAAAATCCATGTTCCAGTT[C/T]
CTGATGGCCAAGTATGCTCTGTGCTCAAGTTCTACAGGGAGTCGACATGGCTTCCCGTAAACTATCTGATGTGGGGACATTCTAATGGGTGTCTTGTATG

Reverse complement sequence

CATACAAGACACCCATTAGAATGTCCCCACATCAGATAGTTTACGGGAAGCCATGTCGACTCCCTGTAGAACTTGAGCACAGAGCATACTTGGCCATCAG[G/A]
AACTGGAACATGGATTTTGAGGGAGCAGGAGAATGGAGAAAAATGCAGATCGCTGAACTTGAGGAATGGAGAGAAAAGACTTACCACAACACAAAGATAT

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.10%	30.30%	0.23%	4.36%	NA
All Indica	2759	95.50%	4.30%	0.04%	0.11%	NA
All Japonica	1512	24.10%	62.30%	0.53%	13.03%	NA
Aus	269	1.90%	98.10%	0.00%	0.00%	NA
Indica I	595	97.30%	2.70%	0.00%	0.00%	NA
Indica II	465	98.30%	1.50%	0.00%	0.22%	NA
Indica III	913	95.20%	4.50%	0.11%	0.22%	NA
Indica Intermediate	786	93.00%	7.00%	0.00%	0.00%	NA
Temperate Japonica	767	6.80%	88.90%	0.26%	4.04%	NA
Tropical Japonica	504	47.20%	21.60%	1.19%	29.96%	NA
Japonica Intermediate	241	31.10%	62.70%	0.00%	6.22%	NA
VI/Aromatic	96	24.00%	71.90%	2.08%	2.08%	NA
Intermediate	90	52.20%	43.30%	0.00%	4.44%	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
vg1008769988	C -> T	LOC_Os10g17400.1	synonymous_variant ; p.Arg856Arg; LOW	synonymous_codon	Average:49.066; most accessible tissue: Zhenshan97 young leaf, score: 71.923	N	N	N	N
vg1008769988	C -> DEL	LOC_Os10g17400.1	N	frameshift_variant	Average:49.066; most accessible tissue: Zhenshan97 young leaf, score: 71.923	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
vg1008769988	NA	2.92E-14	mr1013	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
vg1008769988	NA	1.61E-12	mr1031	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
vg1008769988	NA	1.32E-07	mr1045	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
vg1008769988	NA	5.47E-13	mr1056	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
vg1008769988	NA	4.58E-06	mr1118	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
vg1008769988	NA	6.52E-15	mr1156	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
vg1008769988	NA	7.51E-07	mr1156	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
vg1008769988	NA	2.34E-09	mr1157	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
vg1008769988	NA	1.91E-20	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
vg1008769988	NA	1.78E-06	mr1179	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 37 entries

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Search for Variation information by Variation ID:

Detailed information for vg1008769988:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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