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Detailed information for vg0714252447:

Variant ID: vg0714252447 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14252447
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

GGTGGTGCTTCTCCCTTCAATGCTGCTAGCTCTTTCTCCAAACGATCCAGCTTGTCTTCTAGCTTGCAGATCTTTCCCCGATTCTGGTCTTCACGATCTT[G/A]
AGCGGCTATCACGATCTCAGCGCGGGTTTCATCCATAGCCCATAGCATCTCAACCAAGTGCCTTGTGGTAGCATCATTCTCGATCCCAGCCGGTTCAAGG

Reverse complement sequence

CCTTGAACCGGCTGGGATCGAGAATGATGCTACCACAAGGCACTTGGTTGAGATGCTATGGGCTATGGATGAAACCCGCGCTGAGATCGTGATAGCCGCT[C/T]
AAGATCGTGAAGACCAGAATCGGGGAAAGATCTGCAAGCTAGAAGACAAGCTGGATCGTTTGGAGAAAGAGCTAGCAGCATTGAAGGGAGAAGCACCACC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.90%	0.60%	1.31%	3.13%	NA
All Indica	2759	97.40%	0.00%	0.58%	1.96%	NA
All Japonica	1512	89.70%	1.80%	2.65%	5.89%	NA
Aus	269	97.40%	0.40%	1.86%	0.37%	NA
Indica I	595	98.30%	0.00%	0.34%	1.34%	NA
Indica II	465	98.50%	0.00%	0.22%	1.29%	NA
Indica III	913	95.50%	0.10%	0.77%	3.61%	NA
Indica Intermediate	786	98.30%	0.00%	0.76%	0.89%	NA
Temperate Japonica	767	88.50%	0.00%	0.39%	11.08%	NA
Tropical Japonica	504	92.30%	2.80%	4.56%	0.40%	NA
Japonica Intermediate	241	88.00%	5.40%	5.81%	0.83%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	94.40%	1.10%	1.11%	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
vg0714252447	G -> DEL	LOC_Os07g25010.1	N	frameshift_variant	Average:16.782; most accessible tissue: Callus, score: 26.067	N	N	N	N
vg0714252447	G -> A	LOC_Os07g25010.1	N	stop_gained	Average:16.782; most accessible tissue: Callus, score: 26.067	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714252447	5.11E-07	4.50E-07	mr1117	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
vg0714252447	2.92E-06	9.55E-07	mr1123	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
vg0714252447	2.55E-06	1.81E-06	mr1242	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
vg0714252447	NA	8.15E-06	mr1496	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
vg0714252447	4.19E-06	1.43E-06	mr1117_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
vg0714252447	1.93E-06	NA	mr1118_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
vg0714252447	NA	6.99E-06	mr1119_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
vg0714252447	2.67E-06	2.43E-06	mr1120_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
vg0714252447	4.78E-07	1.71E-06	mr1123_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
vg0714252447	1.57E-06	5.12E-07	mr1240_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
vg0714252447	2.56E-06	2.33E-06	mr1242_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
vg0714252447	NA	9.14E-06	mr1247_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
vg0714252447	2.30E-08	3.53E-09	mr1496_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