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Detailed information for vg1109865508:

Variant ID: vg1109865508 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9865508
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

TGACATGGCGAAGGCGGCTGCGGTGGCAAGGGCACTCCAGACCAAGGCAGAGATCCTTTCGACAAGCCAGCTGCTGGTGCCCCAAGCCGCTCCGTCGCAG[T/C]
CGGCAGCGGCCCCAACTGCGCTCTCCGCTGTGCAAGCCCAAGTCAACCCTGACCCCGAAACACAAACCGAAGCCGACATGGAAGCCATGCGACAGAACAT

Reverse complement sequence

ATGTTCTGTCGCATGGCTTCCATGTCGGCTTCGGTTTGTGTTTCGGGGTCAGGGTTGACTTGGGCTTGCACAGCGGAGAGCGCAGTTGGGGCCGCTGCCG[A/G]
CTGCGACGGAGCGGCTTGGGGCACCAGCAGCTGGCTTGTCGAAAGGATCTCTGCCTTGGTCTGGAGTGCCCTTGCCACCGCAGCCGCCTTCGCCATGTCA

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	49.00%	44.60%	6.16%	0.23%	NA
All Indica	2759	73.80%	19.50%	6.71%	0.04%	NA
All Japonica	1512	2.10%	96.60%	1.19%	0.13%	NA
Aus	269	72.10%	17.50%	10.41%	0.00%	NA
Indica I	595	73.40%	21.30%	5.21%	0.00%	NA
Indica II	465	82.40%	11.60%	6.02%	0.00%	NA
Indica III	913	73.60%	18.60%	7.78%	0.00%	NA
Indica Intermediate	786	69.20%	23.70%	7.00%	0.13%	NA
Temperate Japonica	767	2.10%	96.90%	1.04%	0.00%	NA
Tropical Japonica	504	2.20%	96.80%	0.99%	0.00%	NA
Japonica Intermediate	241	1.70%	95.40%	2.07%	0.83%	NA
VI/Aromatic	96	14.60%	22.90%	55.21%	7.29%	NA
Intermediate	90	44.40%	46.70%	7.78%	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
vg1109865508	T -> DEL	LOC_Os11g17670.1	N	frameshift_variant	Average:14.73; most accessible tissue: Callus, score: 29.289	N	N	N	N
vg1109865508	T -> C	LOC_Os11g17670.1	missense_variant ; p.Ser255Pro; MODERATE	nonsynonymous_codon ; S255P	Average:14.73; most accessible tissue: Callus, score: 29.289	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109865508	NA	1.82E-06	mr1041_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
vg1109865508	NA	1.67E-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
vg1109865508	NA	2.77E-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
vg1109865508	3.77E-06	9.84E-07	mr1341_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
vg1109865508	NA	1.98E-08	mr1418_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
vg1109865508	NA	2.26E-06	mr1419_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
vg1109865508	NA	1.45E-07	mr1420_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
vg1109865508	NA	5.43E-06	mr1428_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
vg1109865508	NA	2.63E-07	mr1467_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
vg1109865508	NA	1.80E-08	mr1488_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
vg1109865508	NA	3.52E-07	mr1492_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
vg1109865508	NA	3.31E-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
vg1109865508	NA	3.88E-07	mr1556_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
vg1109865508	NA	1.93E-07	mr1604_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
vg1109865508	NA	7.66E-06	mr1759_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
vg1109865508	NA	9.46E-07	mr1764_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
vg1109865508	NA	1.94E-07	mr1779_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
vg1109865508	NA	2.57E-06	mr1811_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
vg1109865508	NA	8.26E-06	mr1816_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
vg1109865508	NA	7.64E-06	mr1832_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
vg1109865508	NA	1.02E-07	mr1992_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