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Detailed information for vg0303210296:

Variant ID: vg0303210296 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 3210296
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.61, T: 0.39, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:

CTATCTGCAAACTAACCTTGGTAGTGTGTATAGAGTAACCGAGAATGGCCATCTTTCACCTGGATGGTGGTTCTGCATAGTTCATCAACAGGAGGTACTT[C/T]
AGGCAGGCAAAGCACCTCAAGTATGCATGGCAGCGTGAAACTGCGGTGAATGACTTGGTGGTGAGACTGTTGGTTGTCTGGATGAGAGCACAGCAGTTTC

Reverse complement sequence

GAAACTGCTGTGCTCTCATCCAGACAACCAACAGTCTCACCACCAAGTCATTCACCGCAGTTTCACGCTGCCATGCATACTTGAGGTGCTTTGCCTGCCT[G/A]
AAGTACCTCCTGTTGATGAACTATGCAGAACCACCATCCAGGTGAAAGATGGCCATTCTCGGTTACTCTATACACACTACCAAGGTTAGTTTGCAGATAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.70%	38.20%	0.08%	0.00%	NA
All Indica	2759	93.90%	6.00%	0.14%	0.00%	NA
All Japonica	1512	0.30%	99.70%	0.00%	0.00%	NA
Aus	269	89.20%	10.80%	0.00%	0.00%	NA
Indica I	595	87.60%	12.10%	0.34%	0.00%	NA
Indica II	465	94.40%	5.60%	0.00%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	92.20%	7.50%	0.25%	0.00%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	0.00%	100.00%	0.00%	0.00%	NA
Japonica Intermediate	241	0.80%	99.20%	0.00%	0.00%	NA
VI/Aromatic	96	42.70%	57.30%	0.00%	0.00%	NA
Intermediate	90	46.70%	53.30%	0.00%	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
vg0303210296	C -> T	LOC_Os03g06420.1	3_prime_UTR_variant ; 131.0bp to feature; MODIFIER	silent_mutation	Average:81.629; most accessible tissue: Minghui63 flag leaf, score: 93.233	N	N	N	N
vg0303210296	C -> T	LOC_Os03g06420.3	3_prime_UTR_variant ; 131.0bp to feature; MODIFIER	silent_mutation	Average:81.629; most accessible tissue: Minghui63 flag leaf, score: 93.233	N	N	N	N
vg0303210296	C -> T	LOC_Os03g06420.4	3_prime_UTR_variant ; 131.0bp to feature; MODIFIER	silent_mutation	Average:81.629; most accessible tissue: Minghui63 flag leaf, score: 93.233	N	N	N	N
vg0303210296	C -> T	LOC_Os03g06420.2	3_prime_UTR_variant ; 131.0bp to feature; MODIFIER	silent_mutation	Average:81.629; most accessible tissue: Minghui63 flag leaf, score: 93.233	N	N	N	N
vg0303210296	C -> T	LOC_Os03g06410.1	downstream_gene_variant ; 1997.0bp to feature; MODIFIER	silent_mutation	Average:81.629; most accessible tissue: Minghui63 flag leaf, score: 93.233	N	N	N	N
vg0303210296	C -> T	LOC_Os03g06430.1	downstream_gene_variant ; 2463.0bp to feature; MODIFIER	silent_mutation	Average:81.629; most accessible tissue: Minghui63 flag leaf, score: 93.233	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)
vg0303210296	C	T	-0.03	-0.03	-0.04	-0.02	-0.01	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0303210296	NA	1.68E-39	mr1105	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
vg0303210296	NA	2.24E-16	mr1116	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
vg0303210296	NA	3.25E-14	mr1218	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
vg0303210296	NA	3.14E-08	mr1488	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
vg0303210296	NA	5.01E-08	mr1506	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
vg0303210296	NA	1.32E-07	mr1604	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
vg0303210296	NA	4.49E-08	mr1659	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
vg0303210296	NA	7.87E-07	mr1797	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
vg0303210296	NA	7.87E-07	mr1801	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
vg0303210296	NA	5.55E-07	mr1824	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