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Detailed information for vg1221084756:

Variant ID: vg1221084756 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21084756
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, C: 0.06, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

AGGATGTTGGTAACACTGTCATTGAGGTAGGGAAAGAGGGGGAAGACAAAGCAGTAGTGCTATGGAAGTCAGAAGATTTCTCTCAACCAGATATTTTTGA[C/T]
CAGATGTCTCAGGAGGACGACAAAAGTAATGATTTGTTGAAAAGAATGGATGTGGACTTAAAACTTGGGGGTGTGAAACTATTTACTGATGAAGAGGAGG

Reverse complement sequence

CCTCCTCTTCATCAGTAAATAGTTTCACACCCCCAAGTTTTAAGTCCACATCCATTCTTTTCAACAAATCATTACTTTTGTCGTCCTCCTGAGACATCTG[G/A]
TCAAAAATATCTGGTTGAGAGAAATCTTCTGACTTCCATAGCACTACTGCTTTGTCTTCCCCCTCTTTCCCTACCTCAATGACAGTGTTACCAACATCCT

Allele Frequencies:

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	50.80%	20.30%	0.04%	28.82%	NA
All Indica	2759	50.40%	8.80%	0.00%	40.78%	NA
All Japonica	1512	55.40%	43.00%	0.00%	1.59%	NA
Aus	269	14.50%	15.20%	0.74%	69.52%	NA
Indica I	595	79.80%	12.10%	0.00%	8.07%	NA
Indica II	465	45.60%	13.50%	0.00%	40.86%	NA
Indica III	913	36.60%	1.20%	0.00%	62.21%	NA
Indica Intermediate	786	47.10%	12.30%	0.00%	40.59%	NA
Temperate Japonica	767	24.40%	75.00%	0.00%	0.65%	NA
Tropical Japonica	504	94.40%	2.60%	0.00%	2.98%	NA
Japonica Intermediate	241	72.60%	25.70%	0.00%	1.66%	NA
VI/Aromatic	96	87.50%	0.00%	0.00%	12.50%	NA
Intermediate	90	56.70%	27.80%	0.00%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1221084756	C -> DEL	LOC_Os12g34720.1	N	frameshift_variant	Average:50.441; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N
vg1221084756	C -> T	LOC_Os12g34720.1	synonymous_variant ; p.Asp401Asp; LOW	synonymous_codon	Average:50.441; most accessible tissue: Zhenshan97 young leaf, score: 78.644	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221084756	NA	3.70E-15	Grain_length	Jap_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
vg1221084756	NA	4.93E-06	mr1120	Ind_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
vg1221084756	NA	2.05E-08	mr1334	Ind_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
vg1221084756	9.12E-09	1.02E-10	mr1415	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
vg1221084756	9.12E-09	1.02E-10	mr1567	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
vg1221084756	NA	3.71E-07	mr1806	Ind_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
vg1221084756	NA	2.24E-09	mr1980	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
vg1221084756	5.68E-06	NA	mr1334_2	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
vg1221084756	4.27E-07	6.35E-10	mr1334_2	Ind_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
vg1221084756	NA	7.82E-08	mr1338_2	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
vg1221084756	NA	1.94E-06	mr1446_2	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
vg1221084756	NA	5.26E-06	mr1806_2	Ind_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
vg1221084756	NA	2.24E-07	mr1980_2	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