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Detailed information for vg1127289636:

Variant ID: vg1127289636 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27289636
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCACAATTTTTTTCTAATTAGTAGGGTGATTGCTATTTGCTAATCATAAGTGGGGCCCATATCTCTCTCCTATCCTTCTTCTTCTTCCTCACGCACGCG[C/G]
CAGAGTAGAGGAACGGCGCGCGGCCGGCGCGACGACCTGAGCCAGGACGGCTCGGCGTGCAGCAGAAAAAGCGGCGGCGCTCCGCCATGGTCTCACCGCC

Reverse complement sequence

GGCGGTGAGACCATGGCGGAGCGCCGCCGCTTTTTCTGCTGCACGCCGAGCCGTCCTGGCTCAGGTCGTCGCGCCGGCCGCGCGCCGTTCCTCTACTCTG[G/C]
CGCGTGCGTGAGGAAGAAGAAGAAGGATAGGAGAGAGATATGGGCCCCACTTATGATTAGCAAATAGCAATCACCCTACTAATTAGAAAAAAATTGTGGA

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	45.70%	19.30%	4.44%	30.58%	NA
All Indica	2759	50.70%	16.70%	4.02%	28.52%	NA
All Japonica	1512	37.00%	27.30%	4.89%	30.75%	NA
Aus	269	24.20%	7.40%	8.55%	59.85%	NA
Indica I	595	52.40%	36.60%	3.19%	7.73%	NA
Indica II	465	55.10%	15.30%	4.73%	24.95%	NA
Indica III	913	45.10%	4.40%	3.18%	47.32%	NA
Indica Intermediate	786	53.30%	16.90%	5.22%	24.55%	NA
Temperate Japonica	767	11.00%	46.30%	5.87%	36.90%	NA
Tropical Japonica	504	69.60%	4.80%	2.98%	22.62%	NA
Japonica Intermediate	241	51.90%	14.10%	5.81%	28.22%	NA
VI/Aromatic	96	84.40%	4.20%	1.04%	10.42%	NA
Intermediate	90	58.90%	15.60%	1.11%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127289636	C -> DEL	N	N	silent_mutation	Average:67.572; most accessible tissue: Minghui63 young leaf, score: 90.449	N	N	N	N
vg1127289636	C -> G	LOC_Os11g45100.1	upstream_gene_variant ; 167.0bp to feature; MODIFIER	silent_mutation	Average:67.572; most accessible tissue: Minghui63 young leaf, score: 90.449	N	N	N	N
vg1127289636	C -> G	LOC_Os11g45090.1	downstream_gene_variant ; 4591.0bp to feature; MODIFIER	silent_mutation	Average:67.572; most accessible tissue: Minghui63 young leaf, score: 90.449	N	N	N	N
vg1127289636	C -> G	LOC_Os11g45090-LOC_Os11g45100	intergenic_region ; MODIFIER	silent_mutation	Average:67.572; most accessible tissue: Minghui63 young leaf, score: 90.449	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)
vg1127289636	C	G	0.0	0.0	0.0	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127289636	NA	1.97E-06	mr1153_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
vg1127289636	NA	4.33E-06	mr1262_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
vg1127289636	NA	3.25E-07	mr1376_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
vg1127289636	4.51E-06	4.50E-06	mr1424_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
vg1127289636	NA	7.94E-06	mr1562_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
vg1127289636	4.75E-06	4.75E-06	mr1787_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
vg1127289636	NA	3.06E-07	mr1830_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
vg1127289636	NA	9.00E-06	mr1869_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