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Detailed information for vg0127820806:

Variant ID: vg0127820806 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 27820806
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

GGGTTGCTCAACTTCTGCATTGCGGGAAGCAGTACGGTGCGAACGGTTGCTGTGGTGAGACTGCTGATTAGCTGACTCATGATTTGCTTCTGGCTCAACT[C/T]
TACCTTCCTCAAAACCGAAGCGGGCTGGTGCATGAGCAGCACGGCGGGGGCGGCTAGCCATCTAAACTCCCAGAAGAAGGCGAGGTAAGAATCATATAAG

Reverse complement sequence

CTTATATGATTCTTACCTCGCCTTCTTCTGGGAGTTTAGATGGCTAGCCGCCCCCGCCGTGCTGCTCATGCACCAGCCCGCTTCGGTTTTGAGGAAGGTA[G/A]
AGTTGAGCCAGAAGCAAATCATGAGTCAGCTAATCAGCAGTCTCACCACAGCAACCGTTCGCACCGTACTGCTTCCCGCAATGCAGAAGTTGAGCAACCC

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	49.80%	28.90%	12.04%	9.23%	NA
All Indica	2759	15.60%	48.60%	20.12%	15.73%	NA
All Japonica	1512	99.50%	0.30%	0.13%	0.00%	NA
Aus	269	97.40%	2.20%	0.00%	0.37%	NA
Indica I	595	17.30%	48.40%	21.01%	13.28%	NA
Indica II	465	4.30%	57.00%	17.42%	21.29%	NA
Indica III	913	22.10%	42.40%	20.15%	15.33%	NA
Indica Intermediate	786	13.40%	50.90%	20.99%	14.76%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	2.10%	1.04%	0.00%	NA
Intermediate	90	70.00%	16.70%	12.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0127820806	C -> T	LOC_Os01g48520.1	intron_variant ; MODIFIER	silent_mutation	Average:44.842; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N
vg0127820806	C -> DEL	N	N	silent_mutation	Average:44.842; most accessible tissue: Minghui63 young leaf, score: 59.171	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0127820806	NA	8.20E-18	mr1255	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
vg0127820806	NA	7.49E-09	mr1457	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
vg0127820806	NA	4.06E-08	mr1707	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
vg0127820806	NA	3.61E-12	mr1151_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
vg0127820806	NA	2.27E-09	mr1198_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
vg0127820806	NA	2.09E-07	mr1215_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
vg0127820806	NA	1.96E-07	mr1376_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
vg0127820806	NA	4.75E-08	mr1431_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
vg0127820806	NA	6.99E-06	mr1691_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
vg0127820806	NA	2.62E-08	mr1707_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
vg0127820806	NA	3.48E-11	mr1728_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
vg0127820806	NA	6.73E-10	mr1751_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
vg0127820806	NA	3.34E-08	mr1885_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
vg0127820806	7.73E-06	1.06E-06	mr1980_2	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