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Detailed information for vg0603907011:

Variant ID: vg0603907011 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 3907011
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

TTATATTTTTTTTGGACTTCTTCTTTTTTGGACGCTTAGGACACTTAGTTTTCTTGTGACCCTCCTGGTGACACAACGAGCATCTATTTTGTACCGGCGC[A/T]
GCATCAAGTTGAACGCATGAAGGTGGTTTCCTTCCAGAACCACCCAGACCCGAGTCCATTTCGATCTCCTCTTCCCTCTTGTTTTAATCTTCAAATTTGG

Reverse complement sequence

CCAAATTTGAAGATTAAAACAAGAGGGAAGAGGAGATCGAAATGGACTCGGGTCTGGGTGGTTCTGGAAGGAAACCACCTTCATGCGTTCAACTTGATGC[T/A]
GCGCCGGTACAAAATAGATGCTCGTTGTGTCACCAGGAGGGTCACAAGAAAACTAAGTGTCCTAAGCGTCCAAAAAAGAAGAAGTCCAAAAAAAATATAA

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	88.00%	5.80%	4.27%	1.90%	NA
All Indica	2759	92.60%	1.80%	2.90%	2.72%	NA
All Japonica	1512	79.80%	14.50%	5.69%	0.07%	NA
Aus	269	84.40%	0.40%	11.15%	4.09%	NA
Indica I	595	86.10%	0.80%	6.05%	7.06%	NA
Indica II	465	95.10%	2.40%	2.58%	0.00%	NA
Indica III	913	99.30%	0.40%	0.11%	0.11%	NA
Indica Intermediate	786	88.30%	3.70%	3.94%	4.07%	NA
Temperate Japonica	767	78.60%	13.60%	7.69%	0.13%	NA
Tropical Japonica	504	74.00%	21.60%	4.37%	0.00%	NA
Japonica Intermediate	241	95.40%	2.50%	2.07%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	1.04%	1.04%	NA
Intermediate	90	85.60%	6.70%	5.56%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0603907011	A -> T	LOC_Os06g08070.1	missense_variant ; p.Leu735Gln; MODERATE	nonsynonymous_codon ; L735Q	Average:24.347; most accessible tissue: Zhenshan97 panicle, score: 36.038	unknown	unknown	TOLERATED	0.66
vg0603907011	A -> DEL	LOC_Os06g08070.1	N	frameshift_variant	Average:24.347; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0603907011	5.17E-06	8.01E-08	mr1554	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