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Detailed information for vg1225594396:

Variant ID: vg1225594396 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 25594396
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, C: 0.24, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

AGAAAAAAATCACAGCACACACATATGTGTAAGGATTTGTTCTCACAACCTCCATTTTACCGAAATAACATATTACAAAGAGATTTTTGAAAGTTACATA[T/C]
AAGTTACACTATAGTTACAGTGTAATTACATGTAAGTTACAGTGTAATTACACTACGATTGTACTGTAATTACATCTGTCAAATTTTTGGGAGAAAATTT

Reverse complement sequence

AAATTTTCTCCCAAAAATTTGACAGATGTAATTACAGTACAATCGTAGTGTAATTACACTGTAACTTACATGTAATTACACTGTAACTATAGTGTAACTT[A/G]
TATGTAACTTTCAAAAATCTCTTTGTAATATGTTATTTCGGTAAAATGGAGGTTGTGAGAACAAATCCTTACACATATGTGTGTGCTGTGATTTTTTTCT

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	57.40%	33.60%	0.89%	8.17%	NA
All Indica	2759	39.10%	49.40%	1.05%	10.44%	NA
All Japonica	1512	99.60%	0.10%	0.26%	0.07%	NA
Aus	269	0.70%	68.40%	1.49%	29.37%	NA
Indica I	595	85.90%	13.30%	0.34%	0.50%	NA
Indica II	465	12.30%	78.90%	1.08%	7.74%	NA
Indica III	913	26.00%	50.60%	1.42%	22.02%	NA
Indica Intermediate	786	35.00%	57.80%	1.15%	6.11%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.60%	0.00%	0.40%	0.00%	NA
Japonica Intermediate	241	98.80%	0.40%	0.41%	0.41%	NA
VI/Aromatic	96	72.90%	15.60%	0.00%	11.46%	NA
Intermediate	90	58.90%	27.80%	5.56%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1225594396	T -> C	LOC_Os12g41270.1	intron_variant ; MODIFIER	silent_mutation	Average:19.014; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N
vg1225594396	T -> DEL	N	N	silent_mutation	Average:19.014; most accessible tissue: Zhenshan97 panicle, score: 52.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1225594396	NA	3.28E-07	mr1193	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
vg1225594396	NA	7.19E-06	mr1502	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
vg1225594396	NA	1.04E-06	mr1709	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
vg1225594396	NA	3.08E-07	mr1931	Ind_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
vg1225594396	NA	1.38E-07	mr1057_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
vg1225594396	NA	5.94E-10	mr1170_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
vg1225594396	NA	1.36E-07	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
vg1225594396	NA	2.56E-07	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
vg1225594396	NA	4.97E-06	mr1293_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
vg1225594396	NA	2.42E-07	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
vg1225594396	NA	1.05E-06	mr1508_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
vg1225594396	NA	6.88E-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
vg1225594396	NA	1.00E-08	mr1683_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
vg1225594396	NA	5.68E-06	mr1733_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
vg1225594396	NA	2.19E-06	mr1745_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
vg1225594396	NA	9.50E-06	mr1843_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
vg1225594396	NA	6.68E-07	mr1904_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
vg1225594396	NA	1.65E-06	mr1982_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