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Detailed information for vg0319647611:

Variant ID: vg0319647611 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 19647611
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.53, A: 0.47, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:

TGATTGAAGGCTCGTTCGGCTCGTCTCCATCATCTTGAGTAGCTCCCCACTCGACCTTTGAGTGGGTGCGCTTCGATTCTTCTCCTTCATCATCACTTAC[A/G]
TTGACGACCGGAGGATCCGCTAGGGCTGGGGTAGCTTCTTTTTCCACCACACGAACCTTTGGCGCCAATTGGTAGCGAGGGACGAATAGAGCTCTCTTCC

Reverse complement sequence

GGAAGAGAGCTCTATTCGTCCCTCGCTACCAATTGGCGCCAAAGGTTCGTGTGGTGGAAAAAGAAGCTACCCCAGCCCTAGCGGATCCTCCGGTCGTCAA[T/C]
GTAAGTGATGATGAAGGAGAAGAATCGAAGCGCACCCACTCAAAGGTCGAGTGGGGAGCTACTCAAGATGATGGAGACGAGCCGAACGAGCCTTCAATCA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.00%	31.40%	18.26%	8.25%	NA
All Indica	2759	23.60%	44.30%	24.94%	7.18%	NA
All Japonica	1512	76.60%	5.70%	5.56%	12.17%	NA
Aus	269	17.80%	54.60%	27.14%	0.37%	NA
Indica I	595	17.80%	46.60%	32.94%	2.69%	NA
Indica II	465	20.20%	49.70%	20.43%	9.68%	NA
Indica III	913	29.70%	44.40%	19.28%	6.68%	NA
Indica Intermediate	786	23.00%	39.20%	28.12%	9.67%	NA
Temperate Japonica	767	87.70%	0.00%	3.26%	9.00%	NA
Tropical Japonica	504	59.70%	14.30%	9.13%	16.87%	NA
Japonica Intermediate	241	76.30%	5.80%	5.39%	12.45%	NA
VI/Aromatic	96	76.00%	17.70%	4.17%	2.08%	NA
Intermediate	90	62.20%	16.70%	15.56%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0319647611	A -> DEL	LOC_Os03g35440.1	N	frameshift_variant	Average:13.644; most accessible tissue: Minghui63 young leaf, score: 28.65	N	N	N	N
vg0319647611	A -> G	LOC_Os03g35440.1	synonymous_variant ; p.Asn224Asn; LOW	synonymous_codon	Average:13.644; most accessible tissue: Minghui63 young leaf, score: 28.65	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0319647611	4.66E-06	4.66E-06	mr1320_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