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Detailed information for vg0607378867:

Variant ID: vg0607378867 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 7378867
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGTCGCATTATTTTATTATTTCCAGGGATAAAAGAGGTGAGATAGTTTTCTAAATACCCGGATTGCCCCTTCTCTTTCCTTCTTTTTCTCCTTCTCCTT[T/C]
CTTCTTTTCCCCCTTCCCGTTGACATCGTCGGGAACGGCATGACGGCCTCAGAGAGCAGTGGGGCGAGGTCAGCACGACGTGGTGCGATAACACTGGTGG

Reverse complement sequence

CCACCAGTGTTATCGCACCACGTCGTGCTGACCTCGCCCCACTGCTCTCTGAGGCCGTCATGCCGTTCCCGACGATGTCAACGGGAAGGGGGAAAAGAAG[A/G]
AAGGAGAAGGAGAAAAAGAAGGAAAGAGAAGGGGCAATCCGGGTATTTAGAAAACTATCTCACCTCTTTTATCCCTGGAAATAATAAAATAATGCGACCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	39.70%	0.60%	0.76%	58.97%	NA
All Indica	2759	4.60%	0.20%	0.58%	94.60%	NA
All Japonica	1512	98.40%	0.10%	0.07%	1.39%	NA
Aus	269	69.10%	0.00%	4.46%	26.39%	NA
Indica I	595	4.00%	0.00%	0.34%	95.63%	NA
Indica II	465	4.10%	0.20%	0.22%	95.48%	NA
Indica III	913	3.20%	0.10%	0.66%	96.06%	NA
Indica Intermediate	786	7.10%	0.40%	0.89%	91.60%	NA
Temperate Japonica	767	98.80%	0.00%	0.13%	1.04%	NA
Tropical Japonica	504	99.00%	0.00%	0.00%	0.99%	NA
Japonica Intermediate	241	95.90%	0.80%	0.00%	3.32%	NA
VI/Aromatic	96	27.10%	16.70%	6.25%	50.00%	NA
Intermediate	90	54.40%	3.30%	1.11%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0607378867	T -> C	LOC_Os06g13420.1	missense_variant ; p.Glu236Gly; MODERATE	nonsynonymous_codon ; E236G	Average:26.613; most accessible tissue: Callus, score: 44.026	unknown	unknown	TOLERATED	0.57
vg0607378867	T -> DEL	LOC_Os06g13420.1	N	frameshift_variant	Average:26.613; most accessible tissue: Callus, score: 44.026	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0607378867	3.04E-07	NA	mr1707	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
vg0607378867	2.30E-06	3.54E-06	mr1707	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
vg0607378867	NA	2.98E-06	mr1973	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
vg0607378867	NA	9.34E-14	mr1138_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
vg0607378867	NA	9.92E-07	mr1212_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
vg0607378867	8.20E-07	NA	mr1728_2	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
vg0607378867	NA	5.18E-06	mr1728_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
vg0607378867	3.95E-06	NA	mr1860_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
vg0607378867	NA	4.52E-07	mr1860_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
vg0607378867	3.75E-06	NA	mr1970_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
vg0607378867	1.05E-08	NA	mr1973_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
vg0607378867	2.02E-06	3.23E-10	mr1973_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