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Detailed information for vg1214408077:

Variant ID: vg1214408077 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14408077
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

GAGACAAAGGGTTGCAAAATCCTTTGGAGATGACTACATTGTATACCTCGTGGATGACACTCCAAGAACTATAGAAGAGGCATATTCATCTCCTGACGCT[G/A]
ACTATTGGAAGGAAGCGGTACGCAGTGAAATGGACTCAATTATATCTAATAGTACTTGGGAAGTCGTTGAGCGTCCATATGGGTGCAAGCCTGTAGGATG

Reverse complement sequence

CATCCTACAGGCTTGCACCCATATGGACGCTCAACGACTTCCCAAGTACTATTAGATATAATTGAGTCCATTTCACTGCGTACCGCTTCCTTCCAATAGT[C/T]
AGCGTCAGGAGATGAATATGCCTCTTCTATAGTTCTTGGAGTGTCATCCACGAGGTATACAATGTAGTCATCTCCAAAGGATTTTGCAACCCTTTGTCTC

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	62.80%	29.00%	0.53%	7.68%	NA
All Indica	2759	39.20%	47.10%	0.83%	12.90%	NA
All Japonica	1512	96.70%	2.90%	0.07%	0.33%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	40.70%	17.60%	1.68%	40.00%	NA
Indica II	465	41.10%	55.30%	0.43%	3.23%	NA
Indica III	913	32.40%	64.60%	0.33%	2.63%	NA
Indica Intermediate	786	44.80%	44.10%	1.02%	10.05%	NA
Temperate Japonica	767	95.00%	4.80%	0.00%	0.13%	NA
Tropical Japonica	504	99.00%	0.40%	0.00%	0.60%	NA
Japonica Intermediate	241	97.10%	2.10%	0.41%	0.41%	NA
VI/Aromatic	96	85.40%	14.60%	0.00%	0.00%	NA
Intermediate	90	86.70%	10.00%	1.11%	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
vg1214408077	G -> DEL	LOC_Os12g25080.1	N	frameshift_variant	Average:18.634; most accessible tissue: Minghui63 flag leaf, score: 47.544	N	N	N	N
vg1214408077	G -> A	LOC_Os12g25080.1	missense_variant ; p.Asp548Asn; MODERATE	nonsynonymous_codon ; D548N	Average:18.634; most accessible tissue: Minghui63 flag leaf, score: 47.544	unknown	unknown	TOLERATED	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214408077	7.23E-07	9.59E-09	mr1358_2	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
vg1214408077	1.25E-06	2.37E-06	mr1358_2	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
vg1214408077	NA	5.60E-06	mr1549_2	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
vg1214408077	NA	3.11E-06	mr1578_2	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