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Detailed information for vg0402381225:

Variant ID: vg0402381225 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2381225
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

GGGGCGAATACCAGTGTCCATTCAGCTACGAAGTCAGCTAGCACTTGAGACTTGATAGCAGTGCGTGCAACAAAATGCAAGTCGAACGGGGATAACTCTG[C/T]
CGCCCACTTGCTGAGCCGGCCGGTGACTTCCTTGCCTCGGAGTATTTCGCCCAAAGGGTACTGTGGTGGCACTATGACTTTGTGGGCCTGGAAGTAGTGC

Reverse complement sequence

GCACTACTTCCAGGCCCACAAAGTCATAGTGCCACCACAGTACCCTTTGGGCGAAATACTCCGAGGCAAGGAAGTCACCGGCCGGCTCAGCAAGTGGGCG[G/A]
CAGAGTTATCCCCGTTCGACTTGCATTTTGTTGCACGCACTGCTATCAAGTCTCAAGTGCTAGCTGACTTCGTAGCTGAATGGACACTGGTATTCGCCCC

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	57.80%	23.90%	11.98%	6.39%	NA
All Indica	2759	48.00%	34.90%	15.48%	1.63%	NA
All Japonica	1512	78.20%	1.70%	5.82%	14.29%	NA
Aus	269	45.40%	41.60%	9.29%	3.72%	NA
Indica I	595	58.00%	18.20%	22.52%	1.34%	NA
Indica II	465	41.90%	40.90%	16.13%	1.08%	NA
Indica III	913	46.20%	42.50%	9.64%	1.64%	NA
Indica Intermediate	786	46.10%	35.20%	16.54%	2.16%	NA
Temperate Japonica	767	91.70%	0.30%	3.65%	4.43%	NA
Tropical Japonica	504	63.10%	3.20%	9.72%	24.01%	NA
Japonica Intermediate	241	66.80%	3.30%	4.56%	25.31%	NA
VI/Aromatic	96	54.20%	4.20%	12.50%	29.17%	NA
Intermediate	90	55.60%	25.60%	15.56%	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
vg0402381225	C -> DEL	LOC_Os04g04940.1	N	frameshift_variant	Average:19.753; most accessible tissue: Callus, score: 28.651	N	N	N	N
vg0402381225	C -> T	LOC_Os04g04940.1	missense_variant ; p.Ala760Thr; MODERATE	nonsynonymous_codon ; A760T	Average:19.753; most accessible tissue: Callus, score: 28.651	benign	0.577	TOLERATED	0.10

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402381225	NA	3.81E-07	mr1317	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
vg0402381225	NA	2.41E-07	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
vg0402381225	NA	2.73E-06	mr1414	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
vg0402381225	NA	1.77E-06	mr1608	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
vg0402381225	NA	4.46E-07	mr1830	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
vg0402381225	NA	1.32E-14	mr1846	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
vg0402381225	NA	7.45E-12	mr1846	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
vg0402381225	NA	1.18E-06	mr1317_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
vg0402381225	NA	3.69E-07	mr1608_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
vg0402381225	NA	1.75E-07	mr1608_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
vg0402381225	NA	3.86E-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
vg0402381225	NA	2.29E-11	mr1830_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
vg0402381225	NA	3.69E-08	mr1830_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
vg0402381225	NA	3.01E-22	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
vg0402381225	NA	2.47E-18	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