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Detailed information for vg0706191493:

Variant ID: vg0706191493 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6191493
Reference Allele: T	Alternative Allele: C
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: 94. )

Flanking Sequence (100 bp) in Reference Genome:

CTACTAACAAGTCTTTTAGTGAAGAGTTTAGTAGGATGATGACCAAACGTTTTGAGATGTCCATGATGGGTGAATTGAAGTTCTTCCTCGGCCTTCAAAT[T/C]
AAGCAACTCAAGGAAGGAACTTTCATTTGCCAATCAAAGTATTTGAAGAACATGCTTAAGAAGTTTGGGATGGAGAACGCCAAGCCAATCCACACTCCCA

Reverse complement sequence

TGGGAGTGTGGATTGGCTTGGCGTTCTCCATCCCAAACTTCTTAAGCATGTTCTTCAAATACTTTGATTGGCAAATGAAAGTTCCTTCCTTGAGTTGCTT[A/G]
ATTTGAAGGCCGAGGAAGAACTTCAATTCACCCATCATGGACATCTCAAAACGTTTGGTCATCATCCTACTAAACTCTTCACTAAAAGACTTGTTAGTAG

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	63.00%	14.90%	22.15%	0.00%	NA
All Indica	2759	69.80%	5.00%	25.23%	0.00%	NA
All Japonica	1512	57.30%	36.10%	6.61%	0.00%	NA
Aus	269	10.40%	1.10%	88.48%	0.00%	NA
Indica I	595	59.00%	10.10%	30.92%	0.00%	NA
Indica II	465	83.70%	8.80%	7.53%	0.00%	NA
Indica III	913	72.20%	0.70%	27.16%	0.00%	NA
Indica Intermediate	786	67.00%	3.80%	29.13%	0.00%	NA
Temperate Japonica	767	38.70%	52.00%	9.26%	0.00%	NA
Tropical Japonica	504	86.30%	9.90%	3.77%	0.00%	NA
Japonica Intermediate	241	55.60%	40.20%	4.15%	0.00%	NA
VI/Aromatic	96	95.80%	2.10%	2.08%	0.00%	NA
Intermediate	90	71.10%	16.70%	12.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0706191493	T -> C	LOC_Os07g11240.1	synonymous_variant ; p.Ile1218Ile; LOW	synonymous_codon	Average:25.412; most accessible tissue: Zhenshan97 flag leaf, score: 39.979	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706191493	NA	1.45E-06	mr1097	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
vg0706191493	NA	3.94E-06	mr1149	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
vg0706191493	NA	1.09E-07	mr1252	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
vg0706191493	4.62E-06	NA	mr1419	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
vg0706191493	NA	9.44E-06	mr1576	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
vg0706191493	NA	5.10E-12	mr1626	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
vg0706191493	NA	9.23E-06	mr1626	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
vg0706191493	2.73E-07	NA	mr1773	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
vg0706191493	4.31E-07	4.31E-07	mr1773	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
vg0706191493	1.97E-06	1.97E-06	mr1802	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
vg0706191493	NA	5.74E-06	mr1837	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
vg0706191493	8.76E-06	8.75E-06	mr1994	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
vg0706191493	NA	7.66E-10	mr1011_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