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Detailed information for vg1222365340:

Variant ID: vg1222365340 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22365340
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.89, G: 0.11, others allele: 0.00, population size: 186. )

Flanking Sequence (100 bp) in Reference Genome:

TTAGGATGACTTTATAATTTTATATGATGTTTAAAAAAGTAATTGATTCTTATGGAGGCACAATAGAACTTACATATACATGTTCCACTTCATATGCACT[A/G]
GAGGGATACCAGATGCTTAATAAGCACTGATAAAAAAACAGTAAGGCTTTATATTATGCTCCTAAAGGCTTTGAGATGGATCCACACTATTTATGTTTCT

Reverse complement sequence

AGAAACATAAATAGTGTGGATCCATCTCAAAGCCTTTAGGAGCATAATATAAAGCCTTACTGTTTTTTTATCAGTGCTTATTAAGCATCTGGTATCCCTC[T/C]
AGTGCATATGAAGTGGAACATGTATATGTAAGTTCTATTGTGCCTCCATAAGAATCAATTACTTTTTTAAACATCATATAAAATTATAAAGTCATCCTAA

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	64.60%	29.30%	2.16%	3.87%	NA
All Indica	2759	47.90%	42.50%	3.66%	5.98%	NA
All Japonica	1512	86.80%	12.90%	0.00%	0.33%	NA
Aus	269	96.30%	0.70%	0.00%	2.97%	NA
Indica I	595	30.80%	58.00%	1.51%	9.75%	NA
Indica II	465	22.20%	69.00%	4.73%	4.09%	NA
Indica III	913	74.70%	19.30%	2.85%	3.18%	NA
Indica Intermediate	786	44.90%	42.00%	5.60%	7.51%	NA
Temperate Japonica	767	91.90%	7.70%	0.00%	0.39%	NA
Tropical Japonica	504	78.20%	21.80%	0.00%	0.00%	NA
Japonica Intermediate	241	88.40%	10.80%	0.00%	0.83%	NA
VI/Aromatic	96	96.90%	1.00%	0.00%	2.08%	NA
Intermediate	90	76.70%	18.90%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222365340	A -> DEL	N	N	silent_mutation	Average:50.106; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N
vg1222365340	A -> G	LOC_Os12g36520.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:50.106; most accessible tissue: Minghui63 flag leaf, score: 75.341	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222365340	NA	9.94E-06	mr1013	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
vg1222365340	NA	9.57E-06	mr1015	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
vg1222365340	NA	1.81E-09	mr1011_2	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
vg1222365340	NA	6.86E-06	mr1011_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
vg1222365340	NA	6.89E-06	mr1184_2	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
vg1222365340	NA	1.50E-06	mr1186_2	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
vg1222365340	NA	5.84E-09	mr1220_2	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
vg1222365340	NA	6.90E-06	mr1220_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
vg1222365340	NA	1.62E-06	mr1268_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
vg1222365340	NA	3.12E-06	mr1278_2	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
vg1222365340	NA	1.29E-17	mr1352_2	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
vg1222365340	NA	1.82E-06	mr1682_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
vg1222365340	9.60E-07	9.61E-07	mr1983_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
vg1222365340	8.08E-06	8.08E-06	mr1983_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