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Detailed information for vg1220271730:

Variant ID: vg1220271730 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 20271730
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

GTTGAAATCCGGCTCCCCCAACTACGCATGGTTTGCTTTTGTTTGGCTGAGGTTTGAGGAAGAAGATGCGGCGGAATAGAGCGAAATGCGGCCTAATCCC[C/T]
AGAAAAGCTTCGCAAGCATGGATGAAGTTGGCGATGTGGACTATGGAATTGGGATTTAGGTGATGCAAGCTAATCCCATAGAAATCCAAAATTCCCCGGA

Reverse complement sequence

TCCGGGGAATTTTGGATTTCTATGGGATTAGCTTGCATCACCTAAATCCCAATTCCATAGTCCACATCGCCAACTTCATCCATGCTTGCGAAGCTTTTCT[G/A]
GGGATTAGGCCGCATTTCGCTCTATTCCGCCGCATCTTCTTCCTCAAACCTCAGCCAAACAAAAGCAAACCATGCGTAGTTGGGGGAGCCGGATTTCAAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	50.90%	8.50%	6.43%	34.09%	NA
All Indica	2759	40.10%	11.20%	8.74%	39.98%	NA
All Japonica	1512	71.90%	0.50%	0.99%	26.59%	NA
Aus	269	33.10%	27.10%	10.78%	29.00%	NA
Indica I	595	52.30%	21.70%	7.56%	18.49%	NA
Indica II	465	30.30%	4.70%	7.31%	57.63%	NA
Indica III	913	33.80%	9.00%	10.30%	46.88%	NA
Indica Intermediate	786	44.00%	9.50%	8.65%	37.79%	NA
Temperate Japonica	767	95.20%	0.00%	0.39%	4.43%	NA
Tropical Japonica	504	36.30%	1.20%	1.59%	60.91%	NA
Japonica Intermediate	241	72.20%	0.80%	1.66%	25.31%	NA
VI/Aromatic	96	75.00%	12.50%	9.38%	3.12%	NA
Intermediate	90	57.80%	3.30%	11.11%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1220271730	C -> DEL	LOC_Os12g33560.1	N	frameshift_variant	Average:16.236; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg1220271730	C -> T	LOC_Os12g33560.1	synonymous_variant ; p.Leu107Leu; LOW	synonymous_codon	Average:16.236; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1220271730	NA	2.57E-09	Heading_date	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
vg1220271730	NA	6.22E-06	mr1125	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
vg1220271730	NA	1.30E-06	mr1057_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
vg1220271730	NA	1.57E-08	mr1164_2	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
vg1220271730	NA	4.90E-08	mr1215_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
vg1220271730	NA	5.11E-06	mr1215_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
vg1220271730	NA	3.25E-06	mr1422_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
vg1220271730	NA	2.30E-06	mr1864_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