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Detailed information for vg0825998666:

Variant ID: vg0825998666 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25998666
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCGCATTGTGCTCCCCGGCCGAGATTCTTATTCCGGGCAAGCACTCGCCGATGGCAAGCTTCTGGGTTTCGAGGTAATCAAGTTTGTACTCGATGAAAC[T/C]
AGAGGCCAGCATGCTTGCTGCCGTGTACTCCATATTTGTTGTATGGGGGCACTGGTGGAGAAACCCTTTGTAGTCCCGGTTCGTAACCCCCCTTTAGTCC

Reverse complement sequence

GGACTAAAGGGGGGTTACGAACCGGGACTACAAAGGGTTTCTCCACCAGTGCCCCCATACAACAAATATGGAGTACACGGCAGCAAGCATGCTGGCCTCT[A/G]
GTTTCATCGAGTACAAACTTGATTACCTCGAAACCCAGAAGCTTGCCATCGGCGAGTGCTTGCCCGGAATAAGAATCTCGGCCGGGGAGCACAATGCGAC

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%	35.10%	0.40%	0.00%	NA
All Indica	2759	98.70%	1.20%	0.18%	0.00%	NA
All Japonica	1512	2.90%	97.00%	0.13%	0.00%	NA
Aus	269	81.40%	18.60%	0.00%	0.00%	NA
Indica I	595	99.30%	0.30%	0.34%	0.00%	NA
Indica II	465	98.50%	1.30%	0.22%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	97.10%	2.70%	0.25%	0.00%	NA
Temperate Japonica	767	2.30%	97.50%	0.13%	0.00%	NA
Tropical Japonica	504	2.20%	97.80%	0.00%	0.00%	NA
Japonica Intermediate	241	6.20%	93.40%	0.41%	0.00%	NA
VI/Aromatic	96	11.50%	78.10%	10.42%	0.00%	NA
Intermediate	90	55.60%	42.20%	2.22%	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
vg0825998666	T -> C	LOC_Os08g41150.1	missense_variant ; p.Ser12Gly; MODERATE	nonsynonymous_codon ; S12G	Average:39.217; most accessible tissue: Zhenshan97 young leaf, score: 47.986	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825998666	NA	6.32E-22	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
vg0825998666	NA	4.92E-26	mr1024	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
vg0825998666	NA	8.77E-16	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
vg0825998666	NA	1.69E-20	mr1477	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
vg0825998666	NA	2.22E-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
vg0825998666	NA	2.73E-38	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