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Detailed information for vg0825997637:

Variant ID: vg0825997637 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25997637
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCATCGGTATCTCAATGATATATAGAACCCACATGAGTCAATGACACGTGGGTCAGGATGGCATATCTTAATTTTTACAAAATTATAATGGCATAGCTC[T/C]
AATTTTTCCTTCTTTTATCTCTTCGATAACTAAGGGAAAATTCTGTATAAGAAGAAAGTAGCCGTCGGTGACCACTACCTTCTTGAAGTTGCTCTCCGCC

Reverse complement sequence

GGCGGAGAGCAACTTCAAGAAGGTAGTGGTCACCGACGGCTACTTTCTTCTTATACAGAATTTTCCCTTAGTTATCGAAGAGATAAAAGAAGGAAAAATT[A/G]
GAGCTATGCCATTATAATTTTGTAAAAATTAAGATATGCCATCCTGACCCACGTGTCATTGACTCATGTGGGTTCTATATATCATTGAGATACCGATGAC

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	64.50%	35.30%	0.21%	0.02%	NA
All Indica	2759	98.30%	1.40%	0.29%	0.04%	NA
All Japonica	1512	3.00%	96.90%	0.07%	0.00%	NA
Aus	269	81.00%	19.00%	0.00%	0.00%	NA
Indica I	595	99.30%	0.30%	0.17%	0.17%	NA
Indica II	465	98.30%	1.50%	0.22%	0.00%	NA
Indica III	913	99.50%	0.40%	0.11%	0.00%	NA
Indica Intermediate	786	96.10%	3.30%	0.64%	0.00%	NA
Temperate Japonica	767	2.50%	97.40%	0.13%	0.00%	NA
Tropical Japonica	504	2.20%	97.80%	0.00%	0.00%	NA
Japonica Intermediate	241	6.60%	93.40%	0.00%	0.00%	NA
VI/Aromatic	96	21.90%	78.10%	0.00%	0.00%	NA
Intermediate	90	56.70%	42.20%	1.11%	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
vg0825997637	T -> C	LOC_Os08g41150.1	missense_variant ; p.Arg355Gly; MODERATE	nonsynonymous_codon ; R355G	Average:61.458; most accessible tissue: Zhenshan97 panicle, score: 79.071	unknown	unknown	TOLERATED	0.49
vg0825997637	T -> DEL	LOC_Os08g41150.1	N	frameshift_variant	Average:61.458; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825997637	NA	1.09E-20	mr1021	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
vg0825997637	NA	3.36E-15	mr1323	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
vg0825997637	NA	3.30E-37	mr1601	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
vg0825997637	NA	3.22E-36	mr1689_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