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Detailed information for vg0101949212:

Variant ID: vg0101949212 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 1949212
Reference Allele: G	Alternative Allele: C
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, G: 0.22, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

TGGCGTTCTCCGGCAGCCTGAACCGCCGCATGAACTGCCCGCTGCTGCGCTCCACGCGGTGCCACTTGTCGTTCTTGTCCTCCTTCTCCTTGCTGCGCTG[G/C]
CCGCTGATCACCAGCACGTTGCCTTCCTCCACCTCCACCTTCACCTCCTCCTTCTTGACGCCGGGGAGGTCGGCCTTGAAGACGTGCGACTCCGGCGTCT

Reverse complement sequence

AGACGCCGGAGTCGCACGTCTTCAAGGCCGACCTCCCCGGCGTCAAGAAGGAGGAGGTGAAGGTGGAGGTGGAGGAAGGCAACGTGCTGGTGATCAGCGG[C/G]
CAGCGCAGCAAGGAGAAGGAGGACAAGAACGACAAGTGGCACCGCGTGGAGCGCAGCAGCGGGCAGTTCATGCGGCGGTTCAGGCTGCCGGAGAACGCCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.70%	36.80%	0.30%	0.23%	NA
All Indica	2759	85.20%	14.30%	0.11%	0.40%	NA
All Japonica	1512	35.30%	64.00%	0.73%	0.00%	NA
Aus	269	7.40%	92.60%	0.00%	0.00%	NA
Indica I	595	97.50%	2.20%	0.17%	0.17%	NA
Indica II	465	94.00%	5.80%	0.00%	0.22%	NA
Indica III	913	76.20%	23.30%	0.11%	0.33%	NA
Indica Intermediate	786	81.20%	17.90%	0.13%	0.76%	NA
Temperate Japonica	767	19.90%	78.70%	1.30%	0.00%	NA
Tropical Japonica	504	51.40%	48.40%	0.20%	0.00%	NA
Japonica Intermediate	241	50.60%	49.40%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	61.10%	38.90%	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
vg0101949212	G -> DEL	LOC_Os01g04370.1	N	frameshift_variant	Average:69.879; most accessible tissue: Minghui63 panicle, score: 90.184	N	N	N	N
vg0101949212	G -> C	LOC_Os01g04370.1	synonymous_variant ; p.Gly82Gly; LOW	synonymous_codon	Average:69.879; most accessible tissue: Minghui63 panicle, score: 90.184	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)
vg0101949212	G	C	-0.01	-0.01	-0.01	-0.01	-0.01	0.0