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Detailed information for vg0401709901:

Variant ID: vg0401709901 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1709901
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 51. )

Flanking Sequence (100 bp) in Reference Genome:

TATCAGTGGAGCCATCTGTTCTACAATTCAGCCAGAGCAAAAAGAAGCAGAGCTTTAAGGTCATTTTCAGCATGACCCGCAAATTTCAAGGGGGCTACCT[A/G]
TTTGGGAGCCTAGCATGGTATGATGGAGGCACTCACTATGTCAGGATTCCAATTGCGGTTCGACCAATAGTATCCGATAATTATGCAGATCTCTGAAGAA

Reverse complement sequence

TTCTTCAGAGATCTGCATAATTATCGGATACTATTGGTCGAACCGCAATTGGAATCCTGACATAGTGAGTGCCTCCATCATACCATGCTAGGCTCCCAAA[T/C]
AGGTAGCCCCCTTGAAATTTGCGGGTCATGCTGAAAATGACCTTAAAGCTCTGCTTCTTTTTGCTCTGGCTGAATTGTAGAACAGATGGCTCCACTGATA

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	70.20%	20.80%	1.90%	7.07%	NA
All Indica	2759	94.60%	3.00%	0.54%	1.88%	NA
All Japonica	1512	28.60%	52.40%	3.90%	15.01%	NA
Aus	269	49.40%	30.90%	3.72%	15.99%	NA
Indica I	595	96.80%	3.00%	0.00%	0.17%	NA
Indica II	465	96.10%	1.90%	0.43%	1.51%	NA
Indica III	913	96.70%	1.60%	0.33%	1.31%	NA
Indica Intermediate	786	89.60%	5.10%	1.27%	4.07%	NA
Temperate Japonica	767	29.20%	68.60%	0.13%	2.09%	NA
Tropical Japonica	504	29.20%	32.50%	8.13%	30.16%	NA
Japonica Intermediate	241	25.70%	42.70%	7.05%	24.48%	NA
VI/Aromatic	96	85.40%	7.30%	2.08%	5.21%	NA
Intermediate	90	65.60%	22.20%	4.44%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401709901	A -> DEL	LOC_Os04g03796.2	N	frameshift_variant	Average:60.336; most accessible tissue: Minghui63 flag leaf, score: 85.836	N	N	N	N
vg0401709901	A -> DEL	LOC_Os04g03796.1	N	frameshift_variant	Average:60.336; most accessible tissue: Minghui63 flag leaf, score: 85.836	N	N	N	N
vg0401709901	A -> G	LOC_Os04g03796.1	synonymous_variant ; p.Leu744Leu; LOW	synonymous_codon	Average:60.336; most accessible tissue: Minghui63 flag leaf, score: 85.836	N	N	N	N
vg0401709901	A -> G	LOC_Os04g03796.2	synonymous_variant ; p.Leu384Leu; LOW	synonymous_codon	Average:60.336; most accessible tissue: Minghui63 flag leaf, score: 85.836	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401709901	2.39E-06	2.77E-06	mr1855_2	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