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Detailed information for vg0119596620:

Variant ID: vg0119596620 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 19596620
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGAGTACTCCTACAGCCGCTGTTTGAAGGCGTACTTGCTCTGGCTTTTTGGCTGGGTGATGTTCTGTTGCGGTCACGTGCACGCGGTCGACAAGGGTCT[T/C]
GTGCACTATGCCAGGAGCATCGCTGACGCCGCGGTTGGCGAGGTCCCTCAGTGGAGCTGGGGTTCCGCGTTGTTGGTGGCTCAGTACCGTGGCCTTTGTG

Reverse complement sequence

CACAAAGGCCACGGTACTGAGCCACCAACAACGCGGAACCCCAGCTCCACTGAGGGACCTCGCCAACCGCGGCGTCAGCGATGCTCCTGGCATAGTGCAC[A/G]
AGACCCTTGTCGACCGCGTGCACGTGACCGCAACAGAACATCACCCAGCCAAAAAGCCAGAGCAAGTACGCCTTCAAACAGCGGCTGTAGGAGTACTCGT

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	73.00%	5.60%	12.93%	8.44%	NA
All Indica	2759	78.80%	0.40%	8.95%	11.92%	NA
All Japonica	1512	61.50%	16.60%	21.23%	0.66%	NA
Aus	269	69.10%	0.00%	10.04%	20.82%	NA
Indica I	595	69.10%	0.00%	17.48%	13.45%	NA
Indica II	465	66.20%	1.50%	13.33%	18.92%	NA
Indica III	913	95.00%	0.10%	0.66%	4.27%	NA
Indica Intermediate	786	74.70%	0.30%	9.54%	15.52%	NA
Temperate Japonica	767	38.70%	30.40%	30.77%	0.13%	NA
Tropical Japonica	504	92.10%	0.40%	7.34%	0.20%	NA
Japonica Intermediate	241	70.10%	6.60%	19.92%	3.32%	NA
VI/Aromatic	96	96.90%	0.00%	3.12%	0.00%	NA
Intermediate	90	77.80%	3.30%	14.44%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0119596620	T -> DEL	LOC_Os01g35420.1	N	frameshift_variant	Average:72.06; most accessible tissue: Zhenshan97 young leaf, score: 89.772	N	N	N	N
vg0119596620	T -> C	LOC_Os01g35420.1	synonymous_variant ; p.Leu305Leu; LOW	synonymous_codon	Average:72.06; most accessible tissue: Zhenshan97 young leaf, score: 89.772	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)
vg0119596620	T	C	0.0	0.0	0.0	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0119596620	NA	2.20E-07	mr1164	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
vg0119596620	NA	1.02E-06	mr1205	Jap_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