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Detailed information for vg0301154447:

Variant ID: vg0301154447 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 1154447
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.67, T: 0.33, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

CTGCTACTTTATGCTTCAATTCTGCTACTACGTACTGACACAAATGGAAATCGTCGACGAAGAGTGTGACCGGAGAAGTAAACAAAGGCGGCGATGGCGG[C/T]
GCGCAGCGGCGGCGGTGGCGGCGGAGGTGGAGGCGCTTGGAGCATCTAGCGCCTTCGTATTTCGTATATAGCTCATCATCTCTCTTAAATTAGTCAGTGC

Reverse complement sequence

GCACTGACTAATTTAAGAGAGATGATGAGCTATATACGAAATACGAAGGCGCTAGATGCTCCAAGCGCCTCCACCTCCGCCGCCACCGCCGCCGCTGCGC[G/A]
CCGCCATCGCCGCCTTTGTTTACTTCTCCGGTCACACTCTTCGTCGACGATTTCCATTTGTGTCAGTACGTAGTAGCAGAATTGAAGCATAAAGTAGCAG

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	60.40%	39.40%	0.15%	0.00%	NA
All Indica	2759	97.10%	2.80%	0.07%	0.00%	NA
All Japonica	1512	0.90%	98.90%	0.26%	0.00%	NA
Aus	269	24.50%	75.10%	0.37%	0.00%	NA
Indica I	595	98.30%	1.70%	0.00%	0.00%	NA
Indica II	465	94.40%	5.60%	0.00%	0.00%	NA
Indica III	913	99.20%	0.70%	0.11%	0.00%	NA
Indica Intermediate	786	95.40%	4.50%	0.13%	0.00%	NA
Temperate Japonica	767	0.40%	99.50%	0.13%	0.00%	NA
Tropical Japonica	504	0.80%	99.00%	0.20%	0.00%	NA
Japonica Intermediate	241	2.50%	96.70%	0.83%	0.00%	NA
VI/Aromatic	96	53.10%	46.90%	0.00%	0.00%	NA
Intermediate	90	51.10%	48.90%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0301154447	C -> T	LOC_Os03g02900.1	3_prime_UTR_variant ; 131.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID	Ref	Alt	Root (RT)	Young Leaf (YL)	Flag Leaf (FL)	Young Panicle (YP)	Lemma & Palea (LP)	Stamen & Pistil (SP)
vg0301154447	C	T	-0.05	-0.03	-0.02	0.0	-0.02	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0301154447	NA	6.76E-19	Yield	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
vg0301154447	NA	2.10E-06	mr1020_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
vg0301154447	NA	4.11E-25	mr1024_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
vg0301154447	NA	7.66E-10	mr1349_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
vg0301154447	NA	1.10E-21	mr1401_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
vg0301154447	NA	2.01E-07	mr1567_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
vg0301154447	NA	7.10E-13	mr1666_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
vg0301154447	NA	6.56E-11	mr1728_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
vg0301154447	NA	5.20E-09	mr1835_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
vg0301154447	NA	1.85E-08	mr1940_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