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Detailed information for vg0710393280:

Variant ID: vg0710393280 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10393280
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.86, T: 0.14, others allele: 0.00, population size: 28. )

Flanking Sequence (100 bp) in Reference Genome:

CCGACTGGAGGAAGAGCGACAGTGACAGGAGCGAGAACGACTACAGCATGAGTAACAAGATCGTGAACAGATTGCAAAGGAGGCTGAAGATCGACGACAA[C/T]
GCGCCTTGCAATCTGGGCGGCGAGTGAGAGAGCTCATTGGGCAACAAGACATCGATGGGACAGCGGTCTTTCGCACCCCCCCAGCAGAACGCGGTTGTAG

Reverse complement sequence

CTACAACCGCGTTCTGCTGGGGGGGTGCGAAAGACCGCTGTCCCATCGATGTCTTGTTGCCCAATGAGCTCTCTCACTCGCCGCCCAGATTGCAAGGCGC[G/A]
TTGTCGTCGATCTTCAGCCTCCTTTGCAATCTGTTCACGATCTTGTTACTCATGCTGTAGTCGTTCTCGCTCCTGTCACTGTCGCTCTTCCTCCAGTCGG

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	36.90%	2.80%	0.91%	59.37%	NA
All Indica	2759	8.80%	0.10%	1.16%	89.85%	NA
All Japonica	1512	87.00%	8.50%	0.00%	4.56%	NA
Aus	269	50.60%	0.00%	2.23%	47.21%	NA
Indica I	595	11.80%	0.30%	0.84%	87.06%	NA
Indica II	465	8.00%	0.00%	1.94%	90.11%	NA
Indica III	913	3.00%	0.20%	0.77%	96.06%	NA
Indica Intermediate	786	14.00%	0.00%	1.40%	84.61%	NA
Temperate Japonica	767	81.50%	16.70%	0.00%	1.83%	NA
Tropical Japonica	504	90.30%	0.00%	0.00%	9.72%	NA
Japonica Intermediate	241	97.50%	0.00%	0.00%	2.49%	NA
VI/Aromatic	96	9.40%	0.00%	5.21%	85.42%	NA
Intermediate	90	44.40%	1.10%	0.00%	54.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0710393280	C -> DEL	LOC_Os07g17600.1	N	frameshift_variant	Average:18.602; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0710393280	C -> T	LOC_Os07g17600.1	synonymous_variant ; p.Asn92Asn; LOW	synonymous_codon	Average:18.602; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0710393280	NA	2.30E-06	mr1046_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
vg0710393280	3.69E-06	3.69E-06	mr1365_2	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
vg0710393280	NA	2.85E-06	mr1381_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
vg0710393280	NA	4.37E-06	mr1533_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
vg0710393280	NA	1.63E-06	mr1743_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
vg0710393280	NA	1.99E-06	mr1870_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
vg0710393280	NA	3.67E-06	mr1943_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
vg0710393280	NA	5.25E-06	mr1980_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