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Detailed information for vg0818628912:

Variant ID: vg0818628912 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18628912
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

CTCTATCAACCACGTGCATCAATTCTAGCCTTAGTATCCCGCATGATATCTGACCACCACGAACATCGTCTTACCACTAAGCCGACTCCCGGTCCATCAC[T/C]
GCAAATACTCTCCCGAGGCATCAAGTCACCTACACATGAAACAAACAAAGAAACCATATTCCGAGACCAACCTATCACCAACTTGAGTCATTGTTAGCAA

Reverse complement sequence

TTGCTAACAATGACTCAAGTTGGTGATAGGTTGGTCTCGGAATATGGTTTCTTTGTTTGTTTCATGTGTAGGTGACTTGATGCCTCGGGAGAGTATTTGC[A/G]
GTGATGGACCGGGAGTCGGCTTAGTGGTAAGACGATGTTCGTGGTGGTCAGATATCATGCGGGATACTAAGGCTAGAATTGATGCACGTGGTTGATAGAG

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	89.50%	5.40%	0.57%	4.55%	NA
All Indica	2759	91.60%	2.30%	0.54%	5.58%	NA
All Japonica	1512	86.90%	12.40%	0.60%	0.07%	NA
Aus	269	79.20%	0.00%	0.74%	20.07%	NA
Indica I	595	82.00%	0.00%	0.34%	17.65%	NA
Indica II	465	95.90%	0.20%	0.43%	3.44%	NA
Indica III	913	92.80%	6.10%	1.10%	0.00%	NA
Indica Intermediate	786	94.90%	0.80%	0.13%	4.20%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	65.30%	33.30%	1.39%	0.00%	NA
Japonica Intermediate	241	90.50%	8.30%	0.83%	0.41%	NA
VI/Aromatic	96	94.80%	1.00%	0.00%	4.17%	NA
Intermediate	90	93.30%	3.30%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0818628912	T -> C	LOC_Os08g30280.1	missense_variant ; p.Ser200Gly; MODERATE	nonsynonymous_codon ; S200G	Average:29.088; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	unknown	unknown	TOLERATED	1.00
vg0818628912	T -> DEL	LOC_Os08g30280.1	N	frameshift_variant	Average:29.088; most accessible tissue: Zhenshan97 flag leaf, score: 42.807	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818628912	NA	2.00E-06	mr1073	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
vg0818628912	NA	2.16E-06	mr1227	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
vg0818628912	1.87E-06	2.13E-06	mr1266	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
vg0818628912	1.27E-08	1.27E-08	mr1266	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
vg0818628912	NA	4.79E-07	mr1345	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
vg0818628912	9.03E-06	NA	mr1358	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
vg0818628912	NA	1.92E-06	mr1382	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
vg0818628912	NA	1.63E-06	mr1382	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
vg0818628912	NA	6.70E-06	mr1700	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
vg0818628912	NA	5.05E-08	mr1830	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
vg0818628912	NA	3.76E-09	mr1852	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
vg0818628912	8.63E-06	8.62E-06	mr1873	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
vg0818628912	NA	1.56E-08	mr1047_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
vg0818628912	NA	1.27E-07	mr1808_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
vg0818628912	NA	4.99E-06	mr1870_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