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Detailed information for vg0114587058:

Variant ID: vg0114587058 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14587058
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGATGCGCGCAATCCGTGCGGGCCACCATGCTAGTTTTATTTAAAATAGGAACAAAATGATTCATCCAAATATTGTCAACATAATCGCAGATACAGATT[A/C]
ATGAATTTGTGGACTTAGAAATACCTAGCTCCTAAAAACCTTCGATAGTTGTGCCAAACAAGACTTTAGTAAGCTTTAAGAATGGGACACTCCCATTAAG

Reverse complement sequence

CTTAATGGGAGTGTCCCATTCTTAAAGCTTACTAAAGTCTTGTTTGGCACAACTATCGAAGGTTTTTAGGAGCTAGGTATTTCTAAGTCCACAAATTCAT[T/G]
AATCTGTATCTGCGATTATGTTGACAATATTTGGATGAATCATTTTGTTCCTATTTTAAATAAAACTAGCATGGTGGCCCGCACGGATTGCGCGCATCAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.90%	13.20%	1.59%	21.29%	NA
All Indica	2759	62.90%	0.50%	0.72%	35.88%	NA
All Japonica	1512	57.10%	39.20%	3.57%	0.13%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	47.70%	0.30%	0.84%	51.09%	NA
Indica II	465	68.00%	1.10%	0.65%	30.32%	NA
Indica III	913	69.00%	0.10%	0.55%	30.34%	NA
Indica Intermediate	786	64.20%	0.80%	0.89%	34.10%	NA
Temperate Japonica	767	24.90%	69.00%	6.13%	0.00%	NA
Tropical Japonica	504	99.00%	0.60%	0.20%	0.20%	NA
Japonica Intermediate	241	71.80%	25.30%	2.49%	0.41%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	66.70%	16.70%	1.11%	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
vg0114587058	A -> DEL	N	N	silent_mutation	Average:59.369; most accessible tissue: Zhenshan97 young leaf, score: 71.923	N	N	N	N
vg0114587058	A -> C	LOC_Os01g25740.1	3_prime_UTR_variant ; 491.0bp to feature; MODIFIER	silent_mutation	Average:59.369; most accessible tissue: Zhenshan97 young leaf, score: 71.923	N	N	N	N
vg0114587058	A -> C	LOC_Os01g25730.1	downstream_gene_variant ; 3680.0bp to feature; MODIFIER	silent_mutation	Average:59.369; most accessible tissue: Zhenshan97 young leaf, score: 71.923	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)
vg0114587058	A	C	-0.04	-0.03	-0.02	-0.02	-0.04	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114587058	NA	2.94E-06	mr1582_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