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Detailed information for vg1012224107:

Variant ID: vg1012224107 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 12224107
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, G: 0.01, others allele: 0.00, population size: 65. )

Flanking Sequence (100 bp) in Reference Genome:

AGCGCGAGCAGGATGTGGCCGTGCGCGAGAAGGCTGTTGAACGCTGGCCGGTACGAGGCTTGCTGCGGCCGCTGGTCGCTGGGTCTCGCCGGTATACCTA[C/G]
ATATCCATGATCCTGGGTCTCGCAATGCACGGCCGCGGCGAGGATGCCCTGTCTCTATTCGCCAGCATGCAACGAGCCGGCGTGACGCCGAACGAGGTGA

Reverse complement sequence

TCACCTCGTTCGGCGTCACGCCGGCTCGTTGCATGCTGGCGAATAGAGACAGGGCATCCTCGCCGCGGCCGTGCATTGCGAGACCCAGGATCATGGATAT[G/C]
TAGGTATACCGGCGAGACCCAGCGACCAGCGGCCGCAGCAAGCCTCGTACCGGCCAGCGTTCAACAGCCTTCTCGCGCACGGCCACATCCTGCTCGCGCT

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	31.20%	17.60%	0.99%	50.17%	NA
All Indica	2759	2.60%	28.40%	1.56%	67.45%	NA
All Japonica	1512	89.20%	0.40%	0.07%	10.32%	NA
Aus	269	3.30%	9.30%	0.74%	86.62%	NA
Indica I	595	4.00%	6.90%	2.18%	86.89%	NA
Indica II	465	2.80%	35.90%	2.58%	58.71%	NA
Indica III	913	1.20%	33.50%	1.10%	64.18%	NA
Indica Intermediate	786	3.10%	34.20%	1.02%	61.70%	NA
Temperate Japonica	767	97.00%	0.30%	0.00%	2.74%	NA
Tropical Japonica	504	81.30%	0.40%	0.20%	18.06%	NA
Japonica Intermediate	241	80.90%	0.80%	0.00%	18.26%	NA
VI/Aromatic	96	7.30%	3.10%	0.00%	89.58%	NA
Intermediate	90	42.20%	17.80%	1.11%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1012224107	C -> G	LOC_Os10g23830.1	stop_gained ; p.Tyr67*; HIGH	stop_gained	Average:12.993; most accessible tissue: Callus, score: 37.216	N	N	N	N
vg1012224107	C -> DEL	LOC_Os10g23830.1	N	frameshift_variant	Average:12.993; most accessible tissue: Callus, score: 37.216	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1012224107	NA	1.32E-07	mr1157	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
vg1012224107	NA	3.47E-06	mr1157	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
vg1012224107	NA	1.11E-09	mr1328	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
vg1012224107	NA	3.17E-08	mr1328	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
vg1012224107	NA	3.84E-10	mr1446	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
vg1012224107	7.90E-06	5.62E-08	mr1446	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
vg1012224107	4.90E-07	1.04E-13	mr1446_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
vg1012224107	6.59E-06	2.20E-09	mr1446_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
vg1012224107	NA	3.97E-06	mr1567_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