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Detailed information for vg0126257533:

Variant ID: vg0126257533 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 26257533
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGGTGTTCGACGAGGTCCCCTAGCCTAACCCTGCCCCGCTGCCGCGCCGTCGCCGCTCGCCCGTCACGTCGCCTTGCGCCCCACGCCATGTCACGCCCC[A/G]
AACTAGTCCCGACCGGAACTAGCCCGTGACGCTCCAAATTAACCTGTTAATCGATACCAGTCCCAGGAAACAGTGCTGGTATCACAGGGAGATAGAATAT

Reverse complement sequence

ATATTCTATCTCCCTGTGATACCAGCACTGTTTCCTGGGACTGGTATCGATTAACAGGTTAATTTGGAGCGTCACGGGCTAGTTCCGGTCGGGACTAGTT[T/C]
GGGGCGTGACATGGCGTGGGGCGCAAGGCGACGTGACGGGCGAGCGGCGACGGCGCGGCAGCGGGGCAGGGTTAGGCTAGGGGACCTCGTCGAACACCTG

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	80.20%	17.30%	0.13%	2.41%	NA
All Indica	2759	95.70%	0.30%	0.04%	3.95%	NA
All Japonica	1512	47.70%	52.10%	0.26%	0.00%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	94.10%	0.30%	0.17%	5.38%	NA
Indica II	465	98.90%	0.60%	0.00%	0.43%	NA
Indica III	913	96.60%	0.00%	0.00%	3.40%	NA
Indica Intermediate	786	94.00%	0.40%	0.00%	5.60%	NA
Temperate Japonica	767	8.70%	90.90%	0.39%	0.00%	NA
Tropical Japonica	504	97.80%	2.00%	0.20%	0.00%	NA
Japonica Intermediate	241	66.80%	33.20%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	73.30%	21.10%	1.11%	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
vg0126257533	A -> G	LOC_Os01g46169.1	intron_variant ; MODIFIER	silent_mutation	Average:53.316; most accessible tissue: Zhenshan97 young leaf, score: 88.259	N	N	N	N
vg0126257533	A -> G	LOC_Os01g46169.3	intron_variant ; MODIFIER	silent_mutation	Average:53.316; most accessible tissue: Zhenshan97 young leaf, score: 88.259	N	N	N	N
vg0126257533	A -> G	LOC_Os01g46169.2	intron_variant ; MODIFIER	silent_mutation	Average:53.316; most accessible tissue: Zhenshan97 young leaf, score: 88.259	N	N	N	N
vg0126257533	A -> DEL	N	N	silent_mutation	Average:53.316; most accessible tissue: Zhenshan97 young leaf, score: 88.259	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)
vg0126257533	A	G	0.0	0.01	0.01	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0126257533	NA	9.59E-09	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
vg0126257533	NA	1.97E-06	mr1338	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
vg0126257533	NA	4.44E-06	mr1359	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
vg0126257533	NA	1.41E-09	mr1449	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
vg0126257533	NA	4.06E-12	mr1454	Jap_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
vg0126257533	NA	7.61E-06	mr1129_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