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Detailed information for vg0605916372:

Variant ID: vg0605916372 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 5916372
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAATTACAGAAATAGGCATCTGCTTTAGCACCAACCTCAATGACACTGAGCTATAGCCTGGGACGAACCCAAGGGGTGCCGGGTATGCACTACCCAAAAA[T/G]
TTTGAAAAAAAAACACTAGGGTGTGGCGTGGAATCATGGCAAGGATGGTAGCGAGAAAGCATTAAAATAGAATCCCCTCGATGAATAGAGCACAATGGTG

Reverse complement sequence

CACCATTGTGCTCTATTCATCGAGGGGATTCTATTTTAATGCTTTCTCGCTACCATCCTTGCCATGATTCCACGCCACACCCTAGTGTTTTTTTTTCAAA[A/C]
TTTTTGGGTAGTGCATACCCGGCACCCCTTGGGTTCGTCCCAGGCTATAGCTCAGTGTCATTGAGGTTGGTGCTAAAGCAGATGCCTATTTCTGTAATTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.40%	0.30%	19.91%	11.43%	NA
All Indica	2759	68.30%	0.40%	20.66%	10.69%	NA
All Japonica	1512	77.50%	0.00%	12.30%	10.19%	NA
Aus	269	11.90%	1.10%	60.22%	26.77%	NA
Indica I	595	91.40%	0.00%	7.73%	0.84%	NA
Indica II	465	48.00%	0.60%	32.69%	18.71%	NA
Indica III	913	63.10%	0.50%	22.56%	13.80%	NA
Indica Intermediate	786	68.80%	0.30%	21.12%	9.80%	NA
Temperate Japonica	767	99.20%	0.00%	0.26%	0.52%	NA
Tropical Japonica	504	45.80%	0.00%	29.37%	24.80%	NA
Japonica Intermediate	241	74.70%	0.00%	14.94%	10.37%	NA
VI/Aromatic	96	91.70%	0.00%	3.12%	5.21%	NA
Intermediate	90	61.10%	1.10%	22.22%	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
vg0605916372	T -> G	LOC_Os06g11280.1	upstream_gene_variant ; 2004.0bp to feature; MODIFIER	silent_mutation	Average:83.447; most accessible tissue: Minghui63 root, score: 93.365	N	N	N	N
vg0605916372	T -> G	LOC_Os06g11290.1	downstream_gene_variant ; 1734.0bp to feature; MODIFIER	silent_mutation	Average:83.447; most accessible tissue: Minghui63 root, score: 93.365	N	N	N	N
vg0605916372	T -> G	LOC_Os06g11280-LOC_Os06g11290	intergenic_region ; MODIFIER	silent_mutation	Average:83.447; most accessible tissue: Minghui63 root, score: 93.365	N	N	N	N
vg0605916372	T -> DEL	N	N	silent_mutation	Average:83.447; most accessible tissue: Minghui63 root, score: 93.365	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)
vg0605916372	T	G	-0.03	-0.04	-0.02	0.0	0.0	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0605916372	NA	5.89E-06	mr1211_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
vg0605916372	NA	4.49E-06	mr1363_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
vg0605916372	NA	7.83E-06	mr1819_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
vg0605916372	4.75E-06	6.46E-08	mr1851_2	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
vg0605916372	NA	1.11E-10	mr1864_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
vg0605916372	NA	1.96E-08	mr1952_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