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Detailed information for vg0222677953:

Variant ID: vg0222677953 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22677953
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

TGACCGGCCTCACAACAGCGGTCTGATCGACAGAGCACAAAGTTGGGGATTTCGGTTCCAACGGCTAGTTTTGGTGGTTGGGGGTATATATACCCACTCC[T/C]
TAGCAGCAAGGGTAAGGTTTTGGCACTCCATTGCATTATCTTGAACCCTTGCAAGAGCTCTCACACCCTTGTGCACTTAGTTTATCTAGTGAGGTGTTAG

Reverse complement sequence

CTAACACCTCACTAGATAAACTAAGTGCACAAGGGTGTGAGAGCTCTTGCAAGGGTTCAAGATAATGCAATGGAGTGCCAAAACCTTACCCTTGCTGCTA[A/G]
GGAGTGGGTATATATACCCCCAACCACCAAAACTAGCCGTTGGAACCGAAATCCCCAACTTTGTGCTCTGTCGATCAGACCGCTGTTGTGAGGCCGGTCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	24.30%	19.50%	15.26%	40.96%	NA
All Indica	2759	8.60%	7.70%	19.14%	64.55%	NA
All Japonica	1512	54.60%	42.70%	1.32%	1.39%	NA
Aus	269	3.00%	0.00%	57.62%	39.41%	NA
Indica I	595	18.20%	1.30%	6.72%	73.78%	NA
Indica II	465	2.40%	9.90%	18.28%	69.46%	NA
Indica III	913	3.80%	12.50%	27.71%	55.97%	NA
Indica Intermediate	786	10.60%	5.70%	19.08%	64.63%	NA
Temperate Japonica	767	79.70%	19.70%	0.13%	0.52%	NA
Tropical Japonica	504	19.00%	74.80%	3.17%	2.98%	NA
Japonica Intermediate	241	49.40%	48.50%	1.24%	0.83%	NA
VI/Aromatic	96	45.80%	40.60%	8.33%	5.21%	NA
Intermediate	90	35.60%	27.80%	11.11%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0222677953	T -> DEL	N	N	silent_mutation	Average:21.656; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0222677953	T -> C	LOC_Os02g37580-LOC_Os02g37590	intergenic_region ; MODIFIER	silent_mutation	Average:21.656; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222677953	NA	8.80E-12	mr1069	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
vg0222677953	NA	4.09E-06	mr1072	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
vg0222677953	1.23E-07	NA	mr1098	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
vg0222677953	2.10E-06	NA	mr1099	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
vg0222677953	8.94E-06	NA	mr1067_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
vg0222677953	1.26E-06	NA	mr1072_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
vg0222677953	9.68E-07	NA	mr1075_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
vg0222677953	3.57E-06	NA	mr1077_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
vg0222677953	2.17E-06	NA	mr1098_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
vg0222677953	NA	4.16E-06	mr1782_2	Jap_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