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Detailed information for vg0327526494:

Variant ID: vg0327526494 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 27526494
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, T: 0.07, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

CGATTTCTTTGTGGGCAGACCTGTGGCAGCAGTTCATCGCCAATTTCCAAGGAACTTACAAGCGCCACGCGATTGAAGATGACCTACATGCGTTGACACA[T/G]
AACTCGGGTGAATCCCTACGGGAATTTGTTCGGCGCTTTAACGAGTGCAGGAATACAATCCCTGAGATCACCGACGCTTCTGTAATTCGCGCCTTTAAGT

Reverse complement sequence

ACTTAAAGGCGCGAATTACAGAAGCGTCGGTGATCTCAGGGATTGTATTCCTGCACTCGTTAAAGCGCCGAACAAATTCCCGTAGGGATTCACCCGAGTT[A/C]
TGTGTCAACGCATGTAGGTCATCTTCAATCGCGTGGCGCTTGTAAGTTCCTTGGAAATTGGCGATGAACTGCTGCCACAGGTCTGCCCACAAAGAAATCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.30%	25.70%	3.72%	2.26%	NA
All Indica	2759	67.70%	22.20%	6.23%	3.84%	NA
All Japonica	1512	83.30%	16.50%	0.13%	0.00%	NA
Aus	269	1.90%	98.10%	0.00%	0.00%	NA
Indica I	595	53.40%	26.10%	7.39%	13.11%	NA
Indica II	465	50.30%	37.40%	9.89%	2.37%	NA
Indica III	913	87.30%	9.40%	2.96%	0.33%	NA
Indica Intermediate	786	66.00%	25.20%	7.00%	1.78%	NA
Temperate Japonica	767	70.80%	29.10%	0.13%	0.00%	NA
Tropical Japonica	504	98.40%	1.60%	0.00%	0.00%	NA
Japonica Intermediate	241	91.70%	7.90%	0.41%	0.00%	NA
VI/Aromatic	96	37.50%	62.50%	0.00%	0.00%	NA
Intermediate	90	64.40%	32.20%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0327526494	T -> DEL	LOC_Os03g48330.1	N	frameshift_variant	Average:44.192; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N
vg0327526494	T -> G	LOC_Os03g48330.1	missense_variant ; p.His624Gln; MODERATE	stop_gained	Average:44.192; most accessible tissue: Minghui63 young leaf, score: 61.007	N	N	N	N
vg0327526494	T -> G	LOC_Os03g48330.1	missense_variant ; p.His624Gln; MODERATE	nonsynonymous_codon ; H624Q	Average:44.192; most accessible tissue: Minghui63 young leaf, score: 61.007	benign	-0.592	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0327526494	NA	1.01E-06	mr1126	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
vg0327526494	NA	1.57E-08	mr1157	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
vg0327526494	2.02E-07	NA	mr1309	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
vg0327526494	NA	2.38E-06	mr1320	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
vg0327526494	NA	3.72E-08	mr1321	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
vg0327526494	NA	4.62E-08	mr1328	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
vg0327526494	NA	8.36E-06	mr1331	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
vg0327526494	NA	1.33E-07	mr1393	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
vg0327526494	NA	1.01E-06	mr1400	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
vg0327526494	NA	8.18E-07	mr1438	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
vg0327526494	NA	8.19E-06	mr1444	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
vg0327526494	NA	4.70E-08	mr1446	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
vg0327526494	NA	1.11E-09	mr1539	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
vg0327526494	NA	3.74E-13	mr1540	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
vg0327526494	NA	7.41E-07	mr1621	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
vg0327526494	NA	2.56E-06	mr1727	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
vg0327526494	NA	1.28E-14	mr1732	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
vg0327526494	2.90E-06	NA	mr1900	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
vg0327526494	NA	2.03E-11	mr1409_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
vg0327526494	NA	6.41E-09	mr1582_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
vg0327526494	NA	1.04E-09	mr1649_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