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Detailed information for vg0903048899:

Variant ID: vg0903048899 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 3048899
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTCGAACAAGGTTGAAATGCATACTATACTAGTTTTGATATTCCGCGTTTTGCTGAGGATATGTGGATGAATGCATATTTTATATAATATAAAAGATAG[A/G]
TATATATGTTTAAATAATGTGATAATGATATGGAGATGATAATTTCACATTGCTCGCATATTAAATTCTAAAAATACAACAAAATTATAAATGATATATC

Reverse complement sequence

GATATATCATTTATAATTTTGTTGTATTTTTAGAATTTAATATGCGAGCAATGTGAAATTATCATCTCCATATCATTATCACATTATTTAAACATATATA[T/C]
CTATCTTTTATATTATATAAAATATGCATTCATCCACATATCCTCAGCAAAACGCGGAATATCAAAACTAGTATAGTATGCATTTCAACCTTGTTCGACG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.10%	1.40%	0.36%	1.16%	NA
All Indica	2759	99.70%	0.10%	0.04%	0.18%	NA
All Japonica	1512	94.00%	4.00%	0.99%	0.99%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.60%	0.00%	0.00%	0.44%	NA
Indica Intermediate	786	99.60%	0.30%	0.00%	0.13%	NA
Temperate Japonica	767	99.30%	0.40%	0.26%	0.00%	NA
Tropical Japonica	504	85.90%	10.30%	2.38%	1.39%	NA
Japonica Intermediate	241	93.80%	2.50%	0.41%	3.32%	NA
VI/Aromatic	96	67.70%	0.00%	1.04%	31.25%	NA
Intermediate	90	91.10%	4.40%	0.00%	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
vg0903048899	A -> G	LOC_Os09g06464.1	intron_variant ; MODIFIER	silent_mutation	Average:72.923; most accessible tissue: Zhenshan97 young leaf, score: 92.102	N	N	N	N
vg0903048899	A -> DEL	N	N	silent_mutation	Average:72.923; most accessible tissue: Zhenshan97 young leaf, score: 92.102	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)
vg0903048899	A	G	0.01	0.0	0.01	0.0	0.01	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0903048899	9.56E-06	NA	mr1083	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
vg0903048899	7.82E-07	7.82E-07	mr1085	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
vg0903048899	NA	3.30E-06	mr1104	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
vg0903048899	NA	4.82E-07	mr1155	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
vg0903048899	NA	5.94E-07	mr1213	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
vg0903048899	7.90E-06	NA	mr1233	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
vg0903048899	NA	9.46E-06	mr1437	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
vg0903048899	9.73E-06	NA	mr1104_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