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Detailed information for vg1008407856:

Variant ID: vg1008407856 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 8407856
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

AATATTTCTGTAAAGCCGCCCACAGAATTCGTGGGGCAGATGGATGACTTTTAACAGTAGAATATCAAATCCCTGAAATCTATATTTGCATATCTGAAGT[C/T]
TGCATTAAAACATCTTTCCTACTCGTTAAAAATCTTAAGCAAGATGTTATTTTAGGAACACCATTTTTATCACTTATTCGTCCTTTCCTAGTCACAAACG

Reverse complement sequence

CGTTTGTGACTAGGAAAGGACGAATAAGTGATAAAAATGGTGTTCCTAAAATAACATCTTGCTTAAGATTTTTAACGAGTAGGAAAGATGTTTTAATGCA[G/A]
ACTTCAGATATGCAAATATAGATTTCAGGGATTTGATATTCTACTGTTAAAAGTCATCCATCTGCCCCACGAATTCTGTGGGCGGCTTTACAGAAATATT

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	27.00%	13.50%	53.39%	6.09%	NA
All Indica	2759	34.10%	1.40%	58.75%	5.80%	NA
All Japonica	1512	17.90%	38.50%	36.11%	7.54%	NA
Aus	269	4.80%	0.70%	93.68%	0.74%	NA
Indica I	595	71.10%	0.50%	25.21%	3.19%	NA
Indica II	465	23.00%	1.90%	68.60%	6.45%	NA
Indica III	913	16.80%	1.30%	74.15%	7.78%	NA
Indica Intermediate	786	32.70%	1.80%	60.43%	5.09%	NA
Temperate Japonica	767	5.10%	53.60%	27.77%	13.56%	NA
Tropical Japonica	504	39.70%	8.30%	51.59%	0.40%	NA
Japonica Intermediate	241	12.90%	53.50%	30.29%	3.32%	NA
VI/Aromatic	96	30.20%	0.00%	60.42%	9.38%	NA
Intermediate	90	28.90%	16.70%	51.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1008407856	C -> T	LOC_Os10g16870.1	splice_region_variant&synonymous_variant ; p.Val576Val; LOW	synonymous_codon	Average:15.358; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg1008407856	C -> DEL	LOC_Os10g16870.1	N	frameshift_variant	Average:15.358; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1008407856	6.59E-07	6.60E-07	mr1061	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
vg1008407856	NA	1.74E-07	mr1768_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