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Detailed information for vg1214273942:

Variant ID: vg1214273942 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14273942
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

TGGTGCCCCGCAATGAATCATGCTATGCAAAAGGTAAAGCTGTTGCCCATGCTGGCTTGTGGTTGGCACGGTTAATGTTTCACAACCGAAAATCGTGAAC[C/T]
GGTCCTTAATTGTCATGAGCACTACCATCAAAACCATGTGCTCACAACCCACCATTATCAAGTTTTAGTTGGCACATTAATTAATTAACCAATCACGATA

Reverse complement sequence

TATCGTGATTGGTTAATTAATTAATGTGCCAACTAAAACTTGATAATGGTGGGTTGTGAGCACATGGTTTTGATGGTAGTGCTCATGACAATTAAGGACC[G/A]
GTTCACGATTTTCGGTTGTGAAACATTAACCGTGCCAACCACAAGCCAGCATGGGCAACAGCTTTACCTTTTGCATAGCATGATTCATTGCGGGGCACCA

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	56.60%	26.10%	3.13%	14.18%	NA
All Indica	2759	30.50%	41.30%	5.36%	22.83%	NA
All Japonica	1512	94.00%	3.70%	0.00%	2.31%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	26.90%	33.90%	3.87%	35.29%	NA
Indica II	465	45.80%	23.40%	3.66%	27.10%	NA
Indica III	913	21.40%	56.70%	7.23%	14.68%	NA
Indica Intermediate	786	34.90%	39.40%	5.34%	20.36%	NA
Temperate Japonica	767	96.00%	0.30%	0.00%	3.78%	NA
Tropical Japonica	504	89.30%	10.10%	0.00%	0.60%	NA
Japonica Intermediate	241	97.50%	1.20%	0.00%	1.24%	NA
VI/Aromatic	96	81.20%	18.80%	0.00%	0.00%	NA
Intermediate	90	72.20%	22.20%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214273942	C -> DEL	N	N	silent_mutation	Average:24.75; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N
vg1214273942	C -> T	LOC_Os12g24880-LOC_Os12g24890	intergenic_region ; MODIFIER	silent_mutation	Average:24.75; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214273942	NA	1.29E-06	mr1422	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
vg1214273942	NA	7.26E-06	mr1558	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
vg1214273942	NA	9.78E-09	mr1583	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
vg1214273942	NA	4.67E-06	mr1959	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
vg1214273942	NA	3.75E-06	mr1218_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
vg1214273942	NA	7.54E-06	mr1277_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
vg1214273942	3.48E-06	7.67E-09	mr1422_2	Jap_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
vg1214273942	NA	1.52E-06	mr1583_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
vg1214273942	7.15E-07	5.21E-14	mr1850_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