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Detailed information for vg0905422573:

Variant ID: vg0905422573 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 5422573
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, G: 0.03, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

CGCGTTATGGACTGTATGAATTCACGGTGATGTCGTTCGGTCTGACCAATGCGCCTGCCTTCTTCATGAACTTAATGAACAAAGTGTTCATGGAATACTT[C/G]
GATAAGTTTGTTGTGGTTTTCATTGACGACATCCTGGTGTACTCACAATCAGAGGAAGACCATCAGCAGCATCTCCGTCTGGTATTGGGAAAGTTGCGGG

Reverse complement sequence

CCCGCAACTTTCCCAATACCAGACGGAGATGCTGCTGATGGTCTTCCTCTGATTGTGAGTACACCAGGATGTCGTCAATGAAAACCACAACAAACTTATC[G/C]
AAGTATTCCATGAACACTTTGTTCATTAAGTTCATGAAGAAGGCAGGCGCATTGGTCAGACCGAACGACATCACCGTGAATTCATACAGTCCATAACGCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.50%	0.30%	0.89%	50.25%	NA
All Indica	2759	15.10%	0.50%	1.20%	83.18%	NA
All Japonica	1512	99.30%	0.00%	0.00%	0.73%	NA
Aus	269	82.90%	0.00%	2.97%	14.13%	NA
Indica I	595	12.10%	0.00%	1.34%	86.55%	NA
Indica II	465	18.10%	0.20%	1.08%	80.65%	NA
Indica III	913	10.50%	1.10%	1.20%	87.19%	NA
Indica Intermediate	786	21.00%	0.40%	1.15%	77.48%	NA
Temperate Japonica	767	99.50%	0.00%	0.00%	0.52%	NA
Tropical Japonica	504	99.00%	0.00%	0.00%	0.99%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	63.30%	2.20%	1.11%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0905422573	C -> G	LOC_Os09g09960.1	missense_variant ; p.Phe653Leu; MODERATE	nonsynonymous_codon ; F653L	Average:19.183; most accessible tissue: Minghui63 panicle, score: 34.226	benign	-1.414	TOLERATED	1.00
vg0905422573	C -> DEL	LOC_Os09g09960.1	N	frameshift_variant	Average:19.183; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0905422573	3.06E-06	NA	mr1201	Ind_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