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Detailed information for vg1001448127:

Variant ID: vg1001448127 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1448127
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.75, C: 0.25, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

GAATTAAAACATAAACTTTGGTAATGTAATAATAATGTTCTTATCATCAGTAAGGTGCAAACAAACTCACCTTCTTGGTCGCGGCAAGCTCCTCCTCCAA[T/C]
GCACTAACACGGCTGACGGCAGTCTTTAGCATCTCCTCCTTATCAGCTGGCATTTCTGCAGGCTTGGTGAGAATCGCAATGACCTTCTCCTCGATATCAG

Reverse complement sequence

CTGATATCGAGGAGAAGGTCATTGCGATTCTCACCAAGCCTGCAGAAATGCCAGCTGATAAGGAGGAGATGCTAAAGACTGCCGTCAGCCGTGTTAGTGC[A/G]
TTGGAGGAGGAGCTTGCCGCGACCAAGAAGGTGAGTTTGTTTGCACCTTACTGATGATAAGAACATTATTATTACATTACCAAAGTTTATGTTTTAATTC

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	61.80%	37.80%	0.11%	0.34%	NA
All Indica	2759	40.60%	58.70%	0.11%	0.58%	NA
All Japonica	1512	98.30%	1.60%	0.13%	0.00%	NA
Aus	269	59.10%	40.90%	0.00%	0.00%	NA
Indica I	595	41.30%	58.70%	0.00%	0.00%	NA
Indica II	465	36.80%	61.50%	0.00%	1.72%	NA
Indica III	913	40.10%	59.60%	0.11%	0.22%	NA
Indica Intermediate	786	42.90%	56.10%	0.25%	0.76%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	97.00%	2.80%	0.20%	0.00%	NA
Japonica Intermediate	241	97.50%	2.10%	0.41%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1001448127	T -> C	LOC_Os10g03400.2	synonymous_variant ; p.Ala558Ala; LOW	synonymous_codon	Average:43.37; most accessible tissue: Zhenshan97 young leaf, score: 73.54	N	N	N	N
vg1001448127	T -> DEL	LOC_Os10g03400.2	N	frameshift_variant	Average:43.37; most accessible tissue: Zhenshan97 young leaf, score: 73.54	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001448127	2.12E-07	NA	mr1486	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
vg1001448127	2.61E-10	5.84E-13	mr1486	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
vg1001448127	1.12E-06	NA	mr1548	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
vg1001448127	3.97E-08	2.87E-09	mr1548	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
vg1001448127	NA	2.72E-07	mr1721	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
vg1001448127	8.61E-06	NA	mr1486_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
vg1001448127	8.51E-09	4.08E-11	mr1486_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
vg1001448127	3.70E-10	NA	mr1721_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
vg1001448127	1.84E-10	2.84E-13	mr1721_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