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Detailed information for vg0727264585:

Variant ID: vg0727264585 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 27264585
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: 68. )

Flanking Sequence (100 bp) in Reference Genome:

TGATGTAAGCTGATTCCATAGAAATTTAGTATCCCACGGAAGAACTTCGAGGTTGGAAGAGCAAATCCACCATAAAAGAAATGAGAGAAGACCACGACCT[T/C]
GTGTGTATCAGGGGTCGGAAAAGCCTCACCGCACGCTGGCCGCCACCCGATGATCTCCTTGGCAGGGAGAACGCCGTGCGCCACCATCTCCTTCAGGTTC

Reverse complement sequence

GAACCTGAAGGAGATGGTGGCGCACGGCGTTCTCCCTGCCAAGGAGATCATCGGGTGGCGGCCAGCGTGCGGTGAGGCTTTTCCGACCCCTGATACACAC[A/G]
AGGTCGTGGTCTTCTCTCATTTCTTTTATGGTGGATTTGCTCTTCCAACCTCGAAGTTCTTCCGTGGGATACTAAATTTCTATGGAATCAGCTTACATCA

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	22.70%	12.90%	54.17%	10.24%	NA
All Indica	2759	10.40%	2.20%	73.50%	13.88%	NA
All Japonica	1512	44.20%	34.90%	17.86%	3.04%	NA
Aus	269	23.00%	0.70%	62.83%	13.38%	NA
Indica I	595	7.90%	1.70%	68.57%	21.85%	NA
Indica II	465	6.70%	3.00%	74.19%	16.13%	NA
Indica III	913	8.80%	0.10%	82.48%	8.65%	NA
Indica Intermediate	786	16.40%	4.60%	66.41%	12.60%	NA
Temperate Japonica	767	22.00%	54.80%	20.73%	2.48%	NA
Tropical Japonica	504	73.20%	7.70%	14.48%	4.56%	NA
Japonica Intermediate	241	54.40%	28.20%	15.77%	1.66%	NA
VI/Aromatic	96	28.10%	0.00%	58.33%	13.54%	NA
Intermediate	90	28.90%	23.30%	41.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0727264585	T -> DEL	LOC_Os07g45660.1	N	frameshift_variant	Average:10.07; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0727264585	T -> C	LOC_Os07g45660.1	missense_variant ; p.Lys54Glu; MODERATE	nonsynonymous_codon ; K54E	Average:10.07; most accessible tissue: Minghui63 panicle, score: 20.733	benign	-0.644	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0727264585	NA	1.83E-09	mr1002	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
vg0727264585	NA	7.07E-07	mr1002	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
vg0727264585	NA	5.73E-08	mr1606	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
vg0727264585	NA	2.74E-06	mr1606	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
vg0727264585	9.99E-06	1.22E-12	mr1853	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
vg0727264585	NA	1.81E-08	mr1866	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
vg0727264585	NA	7.41E-06	mr1866	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
vg0727264585	NA	2.34E-08	mr1942	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
vg0727264585	6.10E-06	8.80E-09	mr1942	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
vg0727264585	NA	3.33E-10	mr1002_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
vg0727264585	NA	1.84E-09	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
vg0727264585	NA	2.37E-08	mr1137_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
vg0727264585	NA	5.20E-06	mr1617_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