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Detailed information for vg0714480545:

Variant ID: vg0714480545 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14480545
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: 89. )

Flanking Sequence (100 bp) in Reference Genome:

GGATATTGGATGAAGCCGAAAAGAGAACTAGGAGCAAAGTGTGGCGTATGTACAAAGTACAATGGAGTAATCACACCAAGGATGAAGCCACTTGGGAGAG[C/T]
GAAGAATTCTTGAGGATGGAATACCCGCATCTATTCGAAAACAGGTAAGAAAATCTCGGGACGAGATTTATTTAAGGGGGGTAGGTTTGTAACACCCTGA

Reverse complement sequence

TCAGGGTGTTACAAACCTACCCCCCTTAAATAAATCTCGTCCCGAGATTTTCTTACCTGTTTTCGAATAGATGCGGGTATTCCATCCTCAAGAATTCTTC[G/A]
CTCTCCCAAGTGGCTTCATCCTTGGTGTGATTACTCCATTGTACTTTGTACATACGCCACACTTTGCTCCTAGTTCTCTTTTCGGCTTCATCCAATATCC

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	26.80%	17.60%	6.20%	49.43%	NA
All Indica	2759	2.80%	26.20%	9.28%	61.65%	NA
All Japonica	1512	69.50%	0.50%	0.66%	29.30%	NA
Aus	269	7.10%	30.50%	8.92%	53.53%	NA
Indica I	595	4.20%	12.80%	10.08%	72.94%	NA
Indica II	465	3.90%	35.50%	8.60%	52.04%	NA
Indica III	913	0.80%	26.90%	5.59%	66.70%	NA
Indica Intermediate	786	3.60%	30.20%	13.36%	52.93%	NA
Temperate Japonica	767	63.40%	0.40%	0.52%	35.72%	NA
Tropical Japonica	504	93.50%	0.60%	0.60%	5.36%	NA
Japonica Intermediate	241	39.00%	0.80%	1.24%	58.92%	NA
VI/Aromatic	96	80.20%	0.00%	0.00%	19.79%	NA
Intermediate	90	44.40%	20.00%	3.33%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714480545	C -> DEL	LOC_Os07g25340.1	N	frameshift_variant	Average:11.982; most accessible tissue: Callus, score: 52.441	N	N	N	N
vg0714480545	C -> T	LOC_Os07g25340.1	synonymous_variant ; p.Ser1358Ser; LOW	synonymous_codon	Average:11.982; most accessible tissue: Callus, score: 52.441	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714480545	4.72E-06	5.34E-06	mr1114	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
vg0714480545	4.58E-06	3.94E-06	mr1116	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
vg0714480545	1.64E-07	1.13E-06	mr1117	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
vg0714480545	6.23E-06	6.04E-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
vg0714480545	3.78E-06	1.49E-06	mr1113_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
vg0714480545	7.73E-08	2.25E-07	mr1114_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
vg0714480545	9.54E-10	2.05E-09	mr1117_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
vg0714480545	4.03E-06	2.22E-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
vg0714480545	4.08E-07	6.89E-07	mr1120_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
vg0714480545	8.10E-07	1.57E-06	mr1123_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
vg0714480545	1.51E-07	2.09E-07	mr1240_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
vg0714480545	2.61E-07	4.99E-08	mr1242_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
vg0714480545	1.17E-06	1.22E-06	mr1247_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
vg0714480545	3.83E-08	2.53E-08	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
vg0714480545	1.59E-06	1.05E-06	mr1936_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