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Detailed information for vg0620019428:

Variant ID: vg0620019428 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20019428
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

GGCGGTGCGGCCTGCGCCGTCGGCGGCGGCGGGGCCCGCCGCACCGCCGGGCGACGGCGAGGCGCGCGCCTGCTACGGCATCGTGGTGGCGTGCGTGTCG[C/T]
TGCTGCTGCTGTGCGCGCTCGTCTCCGCCGTCGGCGTCGCCAGGGCCTTCGCCGCCACCGGGGTGCTCGTCCTGCTGCTCGGCCTCGCCGGCTGGCTCGC

Reverse complement sequence

GCGAGCCAGCCGGCGAGGCCGAGCAGCAGGACGAGCACCCCGGTGGCGGCGAAGGCCCTGGCGACGCCGACGGCGGAGACGAGCGCGCACAGCAGCAGCA[G/A]
CGACACGCACGCCACCACGATGCCGTAGCAGGCGCGCGCCTCGCCGTCGCCCGGCGGTGCGGCGGGCCCCGCCGCCGCCGACGGCGCAGGCCGCACCGCC

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	43.70%	24.90%	16.17%	15.15%	NA
All Indica	2759	46.20%	29.70%	11.31%	12.79%	NA
All Japonica	1512	47.20%	2.20%	27.71%	22.82%	NA
Aus	269	0.40%	97.00%	1.49%	1.12%	NA
Indica I	595	46.60%	15.00%	21.18%	17.31%	NA
Indica II	465	41.30%	19.40%	12.90%	26.45%	NA
Indica III	913	45.80%	48.40%	4.05%	1.75%	NA
Indica Intermediate	786	49.40%	25.20%	11.32%	14.12%	NA
Temperate Japonica	767	27.80%	1.40%	38.72%	32.07%	NA
Tropical Japonica	504	64.90%	4.20%	17.06%	13.89%	NA
Japonica Intermediate	241	72.20%	0.80%	14.94%	12.03%	NA
VI/Aromatic	96	36.50%	52.10%	10.42%	1.04%	NA
Intermediate	90	46.70%	16.70%	21.11%	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
vg0620019428	C -> T	LOC_Os06g34400.1	synonymous_variant ; p.Leu37Leu; LOW	synonymous_codon	Average:91.983; most accessible tissue: Minghui63 panicle, score: 98.225	N	N	N	N
vg0620019428	C -> DEL	LOC_Os06g34400.1	N	frameshift_variant	Average:91.983; most accessible tissue: Minghui63 panicle, score: 98.225	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)
vg0620019428	C	T	-0.02	-0.02	-0.03	-0.02	-0.02	-0.01