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Detailed information for vg0210605172:

Variant ID: vg0210605172 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10605172
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.74, A: 0.26, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

TCATTGCCGATCATACAGTAGACTTTTGCTTTGCGGGATATTTTCTCAGCTTCTGCGTCGTCCTCGGGCAACTCTTCGCTGCTTATGAATTTAATGAGTG[A/G]
GGTGCGCCAGTCGTCCGTGGTCTCGATATCGGCAACGGCGCGCTCTGCCTCTGTAGCCCCCGAGCTGATGTCGGGGGCGACCGGGCTATCTTTGCCGCTT

Reverse complement sequence

AAGCGGCAAAGATAGCCCGGTCGCCCCCGACATCAGCTCGGGGGCTACAGAGGCAGAGCGCGCCGTTGCCGATATCGAGACCACGGACGACTGGCGCACC[T/C]
CACTCATTAAATTCATAAGCAGCGAAGAGTTGCCCGAGGACGACGCAGAAGCTGAGAAAATATCCCGCAAAGCAAAAGTCTACTGTATGATCGGCAATGA

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	54.90%	22.50%	16.42%	6.14%	NA
All Indica	2759	29.30%	34.50%	26.13%	10.11%	NA
All Japonica	1512	98.90%	0.70%	0.07%	0.26%	NA
Aus	269	51.30%	31.60%	17.10%	0.00%	NA
Indica I	595	38.20%	35.30%	21.18%	5.38%	NA
Indica II	465	17.80%	45.80%	22.58%	13.76%	NA
Indica III	913	34.30%	24.50%	28.92%	12.27%	NA
Indica Intermediate	786	23.50%	38.70%	28.75%	9.03%	NA
Temperate Japonica	767	99.00%	0.90%	0.00%	0.13%	NA
Tropical Japonica	504	99.00%	0.20%	0.20%	0.60%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	65.60%	17.80%	8.89%	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
vg0210605172	A -> G	LOC_Os02g18290.1	missense_variant ; p.Ser1222Pro; MODERATE	nonsynonymous_codon ; S1222P	Average:29.732; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	possibly damaging	-1.859	TOLERATED	1.00
vg0210605172	A -> DEL	LOC_Os02g18290.1	N	frameshift_variant	Average:29.732; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0210605172	1.85E-06	3.24E-06	mr1901	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
vg0210605172	7.33E-07	3.02E-08	mr1901	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251