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Detailed information for vg0412456522:

Variant ID: vg0412456522 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12456522
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTCCTATATAATAAAGCTTAGTTCCTGAGCATCTGTTTTTCTTCTTTTCTACCCCCCCGTCTGCTCTTCCTCCAGATGGTCTACACCAGGAATGGTAG[C/T]
CGCACAACAGGCGAGGGCAGCAACGGCAAAGAACGCACTGACGGTGTGCATCCCAACAGCGATTCCAGCAATGGTCCGCCACCACTCCCCGAGAATCCGA

Reverse complement sequence

TCGGATTCTCGGGGAGTGGTGGCGGACCATTGCTGGAATCGCTGTTGGGATGCACACCGTCAGTGCGTTCTTTGCCGTTGCTGCCCTCGCCTGTTGTGCG[G/A]
CTACCATTCCTGGTGTAGACCATCTGGAGGAAGAGCAGACGGGGGGGTAGAAAAGAAGAAAAACAGATGCTCAGGAACTAAGCTTTATTATATAGGAATT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.80%	1.70%	2.52%	0.00%	NA
All Indica	2759	94.00%	2.40%	3.59%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	89.60%	3.30%	7.06%	0.00%	NA
Indica I	595	96.50%	0.30%	3.19%	0.00%	NA
Indica II	465	96.10%	1.30%	2.58%	0.00%	NA
Indica III	913	91.10%	4.80%	4.05%	0.00%	NA
Indica Intermediate	786	94.10%	1.90%	3.94%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	3.30%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412456522	C -> T	LOC_Os04g22000.1	synonymous_variant ; p.Ser316Ser; LOW	synonymous_codon	Average:40.99; most accessible tissue: Minghui63 young leaf, score: 55.178	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412456522	2.82E-06	7.48E-06	mr1312	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
vg0412456522	NA	6.64E-06	mr1403	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
vg0412456522	6.21E-06	6.21E-06	mr1463	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
vg0412456522	NA	6.91E-06	mr1569	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
vg0412456522	3.35E-06	NA	mr1669	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
vg0412456522	1.44E-06	7.23E-07	mr1669	Ind_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
vg0412456522	NA	5.92E-06	mr1846	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
vg0412456522	NA	8.91E-06	mr1818_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
vg0412456522	NA	8.28E-14	mr1846_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
vg0412456522	NA	2.08E-11	mr1846_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