RiceVarMap2

Detailed information for vg1218136630:

Variant ID: vg1218136630 (JBrowse)

Variation Type: SNP

Chromosome: chr12

Position: 18136630

Reference Allele: T

Alternative Allele: C

Primary Allele: T

Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.16, others allele: 0.00, population size: 159. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTGAAAGAAAAGGGGTACATACGTCCGAGTACTTCCCCATGGGGTGCTCCTGTGATTTTTGTAGAGAAGAAAGACAAGACGAAGAGGATGTGCGTCGA[T/C]
TACAGAGCTCTCAATGAAGTCACCATCAAAAACAAGTACCCTCTTCCCCGGATCGATGATCTATTCGATCAGCTTAAAGGTGCCACTGTATTCTCCAAGA

Reverse complement sequence

TCTTGGAGAATACAGTGGCACCTTTAAGCTGATCGAATAGATCATCGATCCGGGGAAGAGGGTACTTGTTTTTGATGGTGACTTCATTGAGAGCTCTGTA[A/G]
TCGACGCACATCCTCTTCGTCTTGTCTTTCTTCTCTACAAAAATCACAGGAGCACCCCATGGGGAAGTACTCGGACGTATGTACCCCTTTTCTTTCAACT

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	50.50%	0.10%	11.60%	37.81%	NA
All Indica	2759	38.60%	0.10%	17.58%	43.75%	NA
All Japonica	1512	68.10%	0.00%	2.45%	29.50%	NA
Aus	269	57.20%	0.40%	7.06%	35.32%	NA
Indica I	595	31.80%	0.00%	4.03%	64.20%	NA
Indica II	465	38.90%	0.20%	21.08%	39.78%	NA
Indica III	913	41.60%	0.10%	28.37%	29.90%	NA
Indica Intermediate	786	39.90%	0.10%	13.23%	46.69%	NA
Temperate Japonica	767	76.70%	0.00%	0.39%	22.95%	NA
Tropical Japonica	504	50.60%	0.00%	5.16%	44.25%	NA
Japonica Intermediate	241	77.20%	0.00%	3.32%	19.50%	NA
VI/Aromatic	96	84.40%	0.00%	2.08%	13.54%	NA
Intermediate	90	65.60%	0.00%	5.56%	28.89%	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
vg1218136630	T -> C	LOC_Os12g30214.1	synonymous_variant ; p.Asp944Asp; LOW	synonymous_codon	Average:9.53; most accessible tissue: Callus, score: 20.931	N	N	N	N
vg1218136630	T -> DEL	LOC_Os12g30214.1	N	frameshift_variant	Average:9.53; most accessible tissue: Callus, score: 20.931	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
vg1218136630	NA	4.96E-06	Awn_length	Ind_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
vg1218136630	6.82E-06	2.66E-07	mr1129	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
vg1218136630	1.53E-06	3.72E-08	mr1257	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 3 of 3 entries

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Detailed information for vg1218136630:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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