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Detailed information for vg1125203416:

Variant ID: vg1125203416 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25203416
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.66, T: 0.33, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TTACATTAGGTTATGGATCTCCAGTAATTACAAAGAACTGAACCCGATAGGCTGCTTCTCCATCAGATTTCTAGCAAAAGCAGAACACATCTTTTCTGAT[C/T]
TTAGTTGATGGACATCAAATTTTCTTCAAGATTGCTTCATACCATTCCATTCCACATTGTACAGCTTCCATAAAAGTTGGTTGCACGCATATTTTCATGT

Reverse complement sequence

ACATGAAAATATGCGTGCAACCAACTTTTATGGAAGCTGTACAATGTGGAATGGAATGGTATGAAGCAATCTTGAAGAAAATTTGATGTCCATCAACTAA[G/A]
ATCAGAAAAGATGTGTTCTGCTTTTGCTAGAAATCTGATGGAGAAGCAGCCTATCGGGTTCAGTTCTTTGTAATTACTGGAGATCCATAACCTAATGTAA

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	55.70%	43.70%	0.19%	0.34%	NA
All Indica	2759	82.60%	16.90%	0.14%	0.29%	NA
All Japonica	1512	13.70%	85.70%	0.26%	0.33%	NA
Aus	269	39.80%	59.50%	0.00%	0.74%	NA
Indica I	595	64.50%	35.00%	0.34%	0.17%	NA
Indica II	465	75.90%	23.70%	0.22%	0.22%	NA
Indica III	913	95.00%	4.70%	0.00%	0.33%	NA
Indica Intermediate	786	86.00%	13.50%	0.13%	0.38%	NA
Temperate Japonica	767	3.00%	96.90%	0.13%	0.00%	NA
Tropical Japonica	504	30.20%	68.80%	0.20%	0.79%	NA
Japonica Intermediate	241	13.30%	85.50%	0.83%	0.41%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	43.30%	54.40%	1.11%	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
vg1125203416	C -> T	LOC_Os11g41900.1	intron_variant ; MODIFIER	silent_mutation	Average:49.487; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N
vg1125203416	C -> DEL	N	N	silent_mutation	Average:49.487; most accessible tissue: Minghui63 flag leaf, score: 63.086	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125203416	NA	8.87E-19	mr1133	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
vg1125203416	2.51E-12	NA	mr1191	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
vg1125203416	5.59E-16	4.08E-18	mr1191	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
vg1125203416	1.87E-11	NA	mr1644	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
vg1125203416	4.77E-15	3.73E-19	mr1644	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
vg1125203416	3.04E-12	5.26E-07	mr1662	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
vg1125203416	2.72E-08	2.05E-10	mr1662	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
vg1125203416	NA	7.36E-06	mr1662	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
vg1125203416	NA	6.77E-07	mr1696	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
vg1125203416	NA	1.69E-06	mr1745	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
vg1125203416	NA	1.61E-18	mr1133_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
vg1125203416	NA	4.92E-06	mr1133_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
vg1125203416	1.67E-13	NA	mr1191_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
vg1125203416	1.97E-17	2.40E-25	mr1191_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
vg1125203416	NA	2.19E-07	mr1530_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
vg1125203416	6.86E-10	NA	mr1662_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
vg1125203416	5.80E-06	3.58E-10	mr1662_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
vg1125203416	1.52E-06	2.95E-06	mr1662_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
vg1125203416	NA	1.36E-11	mr1667_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
vg1125203416	NA	3.17E-09	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