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Detailed information for vg0414202857:

Variant ID: vg0414202857 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 14202857
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TCGGCGCGAGCGTGCGCGGGATTGGTGCAAGGCAACACGGCGCTGGCTCGGTCCGGAAATGCTGTTTGGCGATTGCTCGCCCTGGGGAGGGGGTAGCGAT[C/A]
AGATTCGCTCCCCACCTCCCCCCTCCCTCCCTCCACCTATTTCCTTTTTTGTCACCGCATTACTTTCCTATTTTAGTAAATTTATGCACCTAAAATTTAT

Reverse complement sequence

ATAAATTTTAGGTGCATAAATTTACTAAAATAGGAAAGTAATGCGGTGACAAAAAAGGAAATAGGTGGAGGGAGGGAGGGGGGAGGTGGGGAGCGAATCT[G/T]
ATCGCTACCCCCTCCCCAGGGCGAGCAATCGCCAAACAGCATTTCCGGACCGAGCCAGCGCCGTGTTGCCTTGCACCAATCCCGCGCACGCTCGCGCCGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.90%	30.20%	1.44%	3.45%	NA
All Indica	2759	53.00%	40.80%	1.85%	4.35%	NA
All Japonica	1512	82.50%	14.10%	0.79%	2.65%	NA
Aus	269	95.20%	4.80%	0.00%	0.00%	NA
Indica I	595	59.50%	35.30%	1.51%	3.70%	NA
Indica II	465	71.20%	12.70%	3.23%	12.90%	NA
Indica III	913	37.50%	61.80%	0.55%	0.22%	NA
Indica Intermediate	786	55.30%	37.30%	2.80%	4.58%	NA
Temperate Japonica	767	91.30%	3.30%	0.78%	4.69%	NA
Tropical Japonica	504	79.20%	19.60%	0.79%	0.40%	NA
Japonica Intermediate	241	61.40%	36.90%	0.83%	0.83%	NA
VI/Aromatic	96	47.90%	51.00%	1.04%	0.00%	NA
Intermediate	90	63.30%	28.90%	4.44%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0414202857	C -> DEL	N	N	silent_mutation	Average:51.959; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0414202857	C -> A	LOC_Os04g24730.1	downstream_gene_variant ; 4154.0bp to feature; MODIFIER	silent_mutation	Average:51.959; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N
vg0414202857	C -> A	LOC_Os04g24730-LOC_Os04g24750	intergenic_region ; MODIFIER	silent_mutation	Average:51.959; most accessible tissue: Minghui63 panicle, score: 74.563	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0414202857	NA	2.00E-06	mr1066	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
vg0414202857	NA	8.36E-09	mr1280	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
vg0414202857	NA	7.29E-06	mr1298	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
vg0414202857	NA	6.62E-06	mr1337	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
vg0414202857	3.84E-06	4.01E-06	mr1359	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
vg0414202857	NA	1.43E-06	mr1380	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
vg0414202857	NA	6.19E-06	mr1494	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
vg0414202857	1.53E-06	1.35E-09	mr1729	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
vg0414202857	NA	1.92E-08	mr1788	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
vg0414202857	NA	9.07E-06	mr1648_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
vg0414202857	3.20E-06	3.20E-06	mr1651_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
vg0414202857	NA	3.85E-07	mr1655_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
vg0414202857	NA	2.80E-06	mr1669_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
vg0414202857	NA	5.58E-06	mr1977_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