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Detailed information for vg1127845569:

Variant ID: vg1127845569 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27845569
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

GTCAGGATTTGCCTCGGGCCCATTGCGATCGGACCATGGCCATTTTGTTTCATGATGGGCCAGGCAATGGTAACGACCCAATCTGAAAGGCTGGTCCAGT[G/C]
ATAATGGGCTATCTAATATACATCTAAAATAGTATTAATTTGAATTATTTTTTTTGAGAATAATTAAAAATCGGGCATTTTATTCATTAAGAACCAAGTT

Reverse complement sequence

AACTTGGTTCTTAATGAATAAAATGCCCGATTTTTAATTATTCTCAAAAAAAATAATTCAAATTAATACTATTTTAGATGTATATTAGATAGCCCATTAT[C/G]
ACTGGACCAGCCTTTCAGATTGGGTCGTTACCATTGCCTGGCCCATCATGAAACAAAATGGCCATGGTCCGATCGCAATGGGCCCGAGGCAAATCCTGAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.40%	38.20%	2.56%	14.83%	NA
All Indica	2759	36.10%	35.40%	3.77%	24.72%	NA
All Japonica	1512	58.50%	40.30%	0.66%	0.46%	NA
Aus	269	53.90%	42.00%	1.49%	2.60%	NA
Indica I	595	19.80%	56.00%	3.70%	20.50%	NA
Indica II	465	21.10%	18.70%	6.88%	53.33%	NA
Indica III	913	56.40%	31.90%	1.97%	9.75%	NA
Indica Intermediate	786	33.70%	33.80%	4.07%	28.37%	NA
Temperate Japonica	767	42.00%	57.10%	0.78%	0.13%	NA
Tropical Japonica	504	82.50%	15.90%	0.60%	0.99%	NA
Japonica Intermediate	241	61.00%	38.20%	0.41%	0.41%	NA
VI/Aromatic	96	24.00%	74.00%	1.04%	1.04%	NA
Intermediate	90	56.70%	36.70%	2.22%	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
vg1127845569	G -> DEL	N	N	silent_mutation	Average:72.965; most accessible tissue: Callus, score: 97.634	N	N	N	N
vg1127845569	G -> C	LOC_Os11g46000.3	3_prime_UTR_variant ; 758.0bp to feature; MODIFIER	silent_mutation	Average:72.965; most accessible tissue: Callus, score: 97.634	N	N	N	N
vg1127845569	G -> C	LOC_Os11g46000.1	downstream_gene_variant ; 187.0bp to feature; MODIFIER	silent_mutation	Average:72.965; most accessible tissue: Callus, score: 97.634	N	N	N	N
vg1127845569	G -> C	LOC_Os11g46010.1	downstream_gene_variant ; 4923.0bp to feature; MODIFIER	silent_mutation	Average:72.965; most accessible tissue: Callus, score: 97.634	N	N	N	N
vg1127845569	G -> C	LOC_Os11g46000.2	downstream_gene_variant ; 1681.0bp to feature; MODIFIER	silent_mutation	Average:72.965; most accessible tissue: Callus, score: 97.634	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)
vg1127845569	G	C	0.06	0.08	0.05	0.06	0.05	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127845569	1.56E-06	NA	mr1108	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
vg1127845569	NA	1.56E-06	mr1230	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
vg1127845569	4.70E-06	4.70E-06	mr1232	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
vg1127845569	NA	5.31E-06	mr1279	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
vg1127845569	NA	3.87E-07	mr1345	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
vg1127845569	NA	1.24E-06	mr1364	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
vg1127845569	NA	5.18E-06	mr1427	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
vg1127845569	NA	4.35E-08	mr1443	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
vg1127845569	NA	6.68E-06	mr1474	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
vg1127845569	NA	6.68E-06	mr1475	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
vg1127845569	9.39E-07	9.37E-07	mr1562	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
vg1127845569	NA	9.91E-06	mr1606	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
vg1127845569	3.96E-06	1.83E-06	mr1724	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
vg1127845569	NA	4.52E-06	mr1446_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