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Detailed information for vg0411212334:

Variant ID: vg0411212334 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 11212334
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, T: 0.10, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

GAGACCAATGCCCTCTGCCTCCACATCTATAGCAGTTATCCTGCTTTACCCCAGATGATTCACCTGTAACCTTCTTGAGTTCGCCTTTACCTCAGGGTTT[A/T]
CCCTTGCTCTTGCCCTTGAATATGATACTTCCCTTACCTTTCCCTTTCTTCTCACCGTGGCCTCTTTTATGGCCACGCGAGTTTCCAACAACATTGGCAT

Reverse complement sequence

ATGCCAATGTTGTTGGAAACTCGCGTGGCCATAAAAGAGGCCACGGTGAGAAGAAAGGGAAAGGTAAGGGAAGTATCATATTCAAGGGCAAGAGCAAGGG[T/A]
AAACCCTGAGGTAAAGGCGAACTCAAGAAGGTTACAGGTGAATCATCTGGGGTAAAGCAGGATAACTGCTATAGATGTGGAGGCAGAGGGCATTGGTCTC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.90%	4.50%	1.23%	0.42%	NA
All Indica	2759	94.80%	3.00%	1.59%	0.65%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.07%	NA
Aus	269	52.00%	42.80%	5.20%	0.00%	NA
Indica I	595	99.20%	0.20%	0.50%	0.17%	NA
Indica II	465	99.60%	0.20%	0.22%	0.00%	NA
Indica III	913	88.80%	5.90%	3.50%	1.75%	NA
Indica Intermediate	786	95.50%	3.30%	1.02%	0.13%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	88.50%	11.50%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0411212334	A -> DEL	LOC_Os04g20120.1	N	splice_donor_variant	Average:22.074; most accessible tissue: Minghui63 young leaf, score: 38.036	N	N	N	N
vg0411212334	A -> T	LOC_Os04g20120.1	splice_donor_variant&intron_variant ; HIGH	splice_donor_variant	Average:22.074; most accessible tissue: Minghui63 young leaf, score: 38.036	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0411212334	8.84E-07	8.85E-07	mr1487_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