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Detailed information for vg0227578016:

Variant ID: vg0227578016 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 27578016
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCAAACCTCCTCATACCACGGAGGGGTGATACCCGCAGGTACACATGATCTCCTTTTTCAAACTCAAGGTCACGCCTCCGATTGTCAGCGTAATTCTT[T/C]
TGACGGTTCTGCGTTGTCTTTAAACGTTCTCGGATTAGCTTAACTTGTTCTTCTGCTGCCTTGAGTATGTCAGGACCGAATACTAGCGCTTCGCCCACCT

Reverse complement sequence

AGGTGGGCGAAGCGCTAGTATTCGGTCCTGACATACTCAAGGCAGCAGAAGAACAAGTTAAGCTAATCCGAGAACGTTTAAAGACAACGCAGAACCGTCA[A/G]
AAGAATTACGCTGACAATCGGAGGCGTGACCTTGAGTTTGAAAAAGGAGATCATGTGTACCTGCGGGTATCACCCCTCCGTGGTATGAGGAGGTTTGGGA

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	32.50%	17.60%	35.74%	14.22%	NA
All Indica	2759	5.50%	19.60%	51.18%	23.67%	NA
All Japonica	1512	79.70%	8.10%	11.97%	0.20%	NA
Aus	269	15.20%	57.20%	24.54%	2.97%	NA
Indica I	595	3.00%	9.70%	65.55%	21.68%	NA
Indica II	465	3.90%	15.90%	50.32%	29.89%	NA
Indica III	913	7.70%	27.80%	43.92%	20.59%	NA
Indica Intermediate	786	5.90%	19.80%	49.24%	25.06%	NA
Temperate Japonica	767	66.00%	15.30%	18.77%	0.00%	NA
Tropical Japonica	504	95.40%	0.60%	3.37%	0.60%	NA
Japonica Intermediate	241	90.50%	1.20%	8.30%	0.00%	NA
VI/Aromatic	96	97.90%	0.00%	2.08%	0.00%	NA
Intermediate	90	46.70%	13.30%	31.11%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0227578016	T -> DEL	LOC_Os02g45370.1	N	frameshift_variant	Average:8.261; most accessible tissue: Zhenshan97 root, score: 15.132	N	N	N	N
vg0227578016	T -> C	LOC_Os02g45370.1	synonymous_variant ; p.Gln1452Gln; LOW	stop_gained	Average:8.261; most accessible tissue: Zhenshan97 root, score: 15.132	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0227578016	3.07E-06	3.07E-06	mr1914	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
vg0227578016	NA	1.07E-06	mr1184_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
vg0227578016	NA	3.43E-06	mr1278_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
vg0227578016	6.86E-06	4.94E-07	mr1321_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
vg0227578016	NA	1.21E-06	mr1329_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
vg0227578016	NA	7.46E-07	mr1332_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
vg0227578016	4.08E-06	NA	mr1371_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
vg0227578016	8.40E-06	8.40E-06	mr1371_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
vg0227578016	9.70E-07	9.70E-07	mr1445_2	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
vg0227578016	2.18E-06	2.18E-06	mr1499_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
vg0227578016	NA	4.10E-07	mr1524_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
vg0227578016	5.39E-06	NA	mr1645_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
vg0227578016	3.78E-06	3.78E-06	mr1647_2	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
vg0227578016	NA	5.10E-09	mr1690_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