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Detailed information for vg0507044489:

Variant ID: vg0507044489 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7044489
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

TAGAGAGCGGTAGGAACTGACAGGTGGGACCCACTGATTATTTTTTTAAAAAAATGCTGACTAGACTGCCACGTGGACCCAAAACCACTCCGGATTGAGT[C/T]
GGAGGTGTTATTTGTCCAGTTTTAATAGTTGAGGGTGTAGAATATCTGGTTTTCAAGTTCGGGGGTGTAATTCAGTCGACCTCGATAGTTCGGGGGGTAA

Reverse complement sequence

TTACCCCCCGAACTATCGAGGTCGACTGAATTACACCCCCGAACTTGAAAACCAGATATTCTACACCCTCAACTATTAAAACTGGACAAATAACACCTCC[G/A]
ACTCAATCCGGAGTGGTTTTGGGTCCACGTGGCAGTCTAGTCAGCATTTTTTTAAAAAAATAATCAGTGGGTCCCACCTGTCAGTTCCTACCGCTCTCTA

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	69.70%	29.40%	0.15%	0.74%	NA
All Indica	2759	51.30%	47.50%	0.22%	1.05%	NA
All Japonica	1512	99.50%	0.30%	0.00%	0.20%	NA
Aus	269	77.30%	22.70%	0.00%	0.00%	NA
Indica I	595	27.90%	71.90%	0.17%	0.00%	NA
Indica II	465	74.80%	24.50%	0.22%	0.43%	NA
Indica III	913	56.20%	41.80%	0.22%	1.75%	NA
Indica Intermediate	786	49.20%	49.10%	0.25%	1.40%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.60%	0.00%	0.20%	NA
Japonica Intermediate	241	98.80%	0.40%	0.00%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	80.00%	15.60%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0507044489	C -> T	LOC_Os05g12270.1	downstream_gene_variant ; 4130.0bp to feature; MODIFIER	silent_mutation	Average:92.827; most accessible tissue: Zhenshan97 panicle, score: 97.62	N	N	N	N
vg0507044489	C -> T	LOC_Os05g12270-LOC_Os05g12280	intergenic_region ; MODIFIER	silent_mutation	Average:92.827; most accessible tissue: Zhenshan97 panicle, score: 97.62	N	N	N	N
vg0507044489	C -> DEL	N	N	silent_mutation	Average:92.827; most accessible tissue: Zhenshan97 panicle, score: 97.62	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)
vg0507044489	C	T	-0.03	-0.03	-0.03	-0.03	-0.03	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507044489	NA	7.51E-13	mr1195	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
vg0507044489	1.50E-10	1.58E-23	mr1531	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
vg0507044489	1.86E-10	6.09E-15	mr1531	Ind_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
vg0507044489	4.62E-21	1.80E-28	mr1593	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
vg0507044489	9.83E-17	1.15E-32	mr1593	Ind_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
vg0507044489	NA	8.75E-06	mr1686	Ind_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
vg0507044489	NA	4.21E-08	mr1860	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
vg0507044489	NA	8.34E-06	mr1904	Ind_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
vg0507044489	4.56E-09	3.18E-26	mr1195_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
vg0507044489	1.43E-07	5.64E-14	mr1195_2	Ind_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
vg0507044489	NA	8.76E-19	mr1531_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
vg0507044489	NA	5.61E-09	mr1531_2	Ind_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
vg0507044489	3.28E-25	3.28E-35	mr1593_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
vg0507044489	2.11E-19	2.67E-43	mr1593_2	Ind_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