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Detailed information for vg0825541770:

Variant ID: vg0825541770 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25541770
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCTGAGTACTTTTGGTTGTCGTTTGTAGGGATGTCGATGTCGAGGATGTCCAGCAGCGTGGGCAGCCCAAGTTACCGGTGGTCGCCCCGGCGATTACCCT[T/C]
CAAACGCCTATGTCGCAGGACGATATGGGACGAAACTCACCCGTGGAAATGGGCATGGCGATGACCTCCGTAGGTTGGTGATCTTTGTTTTCATCTCCTT

Reverse complement sequence

AAGGAGATGAAAACAAAGATCACCAACCTACGGAGGTCATCGCCATGCCCATTTCCACGGGTGAGTTTCGTCCCATATCGTCCTGCGACATAGGCGTTTG[A/G]
AGGGTAATCGCCGGGGCGACCACCGGTAACTTGGGCTGCCCACGCTGCTGGACATCCTCGACATCGACATCCCTACAAACGACAACCAAAAGTACTCAGG

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	84.50%	2.00%	6.47%	7.02%	NA
All Indica	2759	74.60%	3.30%	10.76%	11.38%	NA
All Japonica	1512	99.00%	0.00%	0.46%	0.53%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	69.10%	2.50%	9.58%	18.82%	NA
Indica II	465	48.00%	7.10%	18.71%	26.24%	NA
Indica III	913	96.40%	0.50%	2.96%	0.11%	NA
Indica Intermediate	786	69.10%	4.80%	16.03%	10.05%	NA
Temperate Japonica	767	98.60%	0.00%	0.65%	0.78%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	98.80%	0.00%	0.83%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	0.00%	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
vg0825541770	T -> C	LOC_Os08g40340.1	missense_variant ; p.Ser581Pro; MODERATE	nonsynonymous_codon ; S581P	Average:27.617; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	unknown	unknown	TOLERATED	0.16
vg0825541770	T -> DEL	LOC_Os08g40340.1	N	frameshift_variant	Average:27.617; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825541770	2.14E-07	6.69E-06	mr1913	Ind_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