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Detailed information for vg0909378209:

Variant ID: vg0909378209 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9378209
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGGTTTTGGGTGTTATGACCATAGTGCCCTTCTTTGACGGAATCATGAATATGCTGGCACAAGGACACGCAGCATTCCTTCCACAGCTCCTATTCCCCT[A/G]
ACACCTGCATATCCAGAATAAAAAATGGGACTAACTTTTAAAATTCAAACCAAAGAAGTCTGGTGCCTATCTCCTCGTCTCCTCCATAGACTGGGGATAT

Reverse complement sequence

ATATCCCCAGTCTATGGAGGAGACGAGGAGATAGGCACCAGACTTCTTTGGTTTGAATTTTAAAAGTTAGTCCCATTTTTTATTCTGGATATGCAGGTGT[T/C]
AGGGGAATAGGAGCTGTGGAAGGAATGCTGCGTGTCCTTGTGCCAGCATATTCATGATTCCGTCAAAGAAGGGCACTATGGTCATAACACCCAAAACCTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.80%	10.10%	4.82%	0.28%	NA
All Indica	2759	98.40%	1.40%	0.18%	0.00%	NA
All Japonica	1512	56.10%	28.50%	14.55%	0.86%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	94.10%	5.50%	0.34%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.30%	0.25%	0.00%	NA
Temperate Japonica	767	39.00%	50.80%	9.52%	0.65%	NA
Tropical Japonica	504	82.90%	2.40%	14.29%	0.40%	NA
Japonica Intermediate	241	54.40%	12.00%	31.12%	2.49%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	11.10%	3.33%	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
vg0909378209	A -> G	LOC_Os09g15340.1	downstream_gene_variant ; 1536.0bp to feature; MODIFIER	silent_mutation	Average:92.759; most accessible tissue: Zhenshan97 flower, score: 96.264	N	N	N	N
vg0909378209	A -> G	LOC_Os09g15330-LOC_Os09g15340	intergenic_region ; MODIFIER	silent_mutation	Average:92.759; most accessible tissue: Zhenshan97 flower, score: 96.264	N	N	N	N
vg0909378209	A -> DEL	N	N	silent_mutation	Average:92.759; most accessible tissue: Zhenshan97 flower, score: 96.264	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)
vg0909378209	A	G	0.08	0.01	0.01	0.05	0.03	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909378209	7.49E-07	2.29E-29	mr1137	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
vg0909378209	NA	9.20E-13	mr1137	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
vg0909378209	NA	1.38E-08	mr1617	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
vg0909378209	1.16E-08	1.08E-34	mr1137_2	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
vg0909378209	NA	4.32E-14	mr1137_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
vg0909378209	NA	1.45E-08	mr1617_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
vg0909378209	NA	1.99E-06	mr1693_2	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