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Detailed information for vg1127814672:

Variant ID: vg1127814672 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27814672
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, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTAATGCACTACTGGAGAAATGATTTTTGCTCGGTGATCCGAAAACTACAATAGTCCCGGTTTGAATAGGAACCAAGACTAAAGAAGATCTTTAGCCC[C/T]
GGTTCAAAAGCGGCACGACACTTTATAATCTTTAGTCCCGGTTGGTAATCATTTTTAGTCCCAGTTCAAAACGTTGTCAGGTCCTCCCCCACTATCTTTA

Reverse complement sequence

TAAAGATAGTGGGGGAGGACCTGACAACGTTTTGAACTGGGACTAAAAATGATTACCAACCGGGACTAAAGATTATAAAGTGTCGTGCCGCTTTTGAACC[G/A]
GGGCTAAAGATCTTCTTTAGTCTTGGTTCCTATTCAAACCGGGACTATTGTAGTTTTCGGATCACCGAGCAAAAATCATTTCTCCAGTAGTGCATTAAAA

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	84.00%	5.60%	1.31%	9.06%	NA
All Indica	2759	74.40%	9.30%	1.81%	14.46%	NA
All Japonica	1512	98.30%	0.30%	0.20%	1.26%	NA
Aus	269	98.90%	0.70%	0.37%	0.00%	NA
Indica I	595	54.10%	4.70%	4.71%	36.47%	NA
Indica II	465	65.60%	22.20%	0.65%	11.61%	NA
Indica III	913	86.30%	3.80%	1.31%	8.54%	NA
Indica Intermediate	786	81.30%	11.50%	0.89%	6.36%	NA
Temperate Japonica	767	97.70%	0.10%	0.00%	2.22%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	0.00%	1.24%	0.83%	NA
VI/Aromatic	96	92.70%	1.00%	6.25%	0.00%	NA
Intermediate	90	82.20%	4.40%	2.22%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127814672	C -> T	LOC_Os11g45970.1	intron_variant ; MODIFIER	silent_mutation	Average:34.988; most accessible tissue: Zhenshan97 young leaf, score: 59.612	N	N	N	N
vg1127814672	C -> DEL	N	N	silent_mutation	Average:34.988; most accessible tissue: Zhenshan97 young leaf, score: 59.612	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127814672	1.96E-06	2.22E-09	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
vg1127814672	1.99E-06	9.22E-11	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
vg1127814672	2.48E-07	2.31E-13	mr1662_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
vg1127814672	2.03E-08	2.29E-14	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