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Detailed information for vg0113518004:

Variant ID: vg0113518004 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13518004
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.59, C: 0.42, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TGGATTTTTCCAAACGGCCACAGCAGATTTTTGCATGCGGGCCTCTCGTCCGTCTGTAATCAGGTGTCTGTGAAAATCATCATTTTTTCATATGGGTATA[T/C]
TGCATGTGAAAACGGACGGTCATCTAAACCAAATGCATGCGAAAATAGTTTTGACCAAAAAACTAAAATTCGTGGGAGAGGGCAGCCGCCGCCGGCCATT

Reverse complement sequence

AATGGCCGGCGGCGGCTGCCCTCTCCCACGAATTTTAGTTTTTTGGTCAAAACTATTTTCGCATGCATTTGGTTTAGATGACCGTCCGTTTTCACATGCA[A/G]
TATACCCATATGAAAAAATGATGATTTTCACAGACACCTGATTACAGACGGACGAGAGGCCCGCATGCAAAAATCTGCTGTGGCCGTTTGGAAAAATCCA

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	73.30%	26.50%	0.23%	0.00%	NA
All Indica	2759	64.40%	35.30%	0.29%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	6.30%	93.30%	0.37%	0.00%	NA
Indica I	595	63.70%	36.00%	0.34%	0.00%	NA
Indica II	465	61.50%	38.30%	0.22%	0.00%	NA
Indica III	913	66.20%	33.70%	0.11%	0.00%	NA
Indica Intermediate	786	64.60%	34.90%	0.51%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	72.20%	25.60%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0113518004	T -> C	LOC_Os01g24010.1	intron_variant ; MODIFIER	silent_mutation	Average:70.588; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113518004	NA	6.95E-06	mr1236	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
vg0113518004	NA	3.59E-07	mr1654	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
vg0113518004	NA	1.34E-06	mr1881	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
vg0113518004	NA	2.27E-15	mr1193_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
vg0113518004	NA	3.97E-06	mr1511_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
vg0113518004	NA	2.46E-13	mr1654_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
vg0113518004	NA	9.14E-09	mr1654_2	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
vg0113518004	NA	2.08E-06	mr1970_2	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