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Detailed information for vg0812056816:

Variant ID: vg0812056816 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 12056816
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGTTCTCCTACAACAACAGTTACCAGGCTAGTCTGCAGATGGCACCCTTTGAAGCACTGTACGGACGGAGGTGCCGCACTTCGCTCTTCTGGGATCAGA[C/T]
AGGGGAACGCCAGTTGTTTGGTACAAAAGTTTTAAATGAGGCAGAAGAGAAAGTCAGAGCTGTCAGGGAAAGATTGAGAATCGCGCAATCTCGACAGAAA

Reverse complement sequence

TTTCTGTCGAGATTGCGCGATTCTCAATCTTTCCCTGACAGCTCTGACTTTCTCTTCTGCCTCATTTAAAACTTTTGTACCAAACAACTGGCGTTCCCCT[G/A]
TCTGATCCCAGAAGAGCGAAGTGCGGCACCTCCGTCCGTACAGTGCTTCAAAGGGTGCCATCTGCAGACTAGCCTGGTAACTGTTGTTGTAGGAGAACTC

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	91.50%	8.50%	0.02%	0.00%	NA
All Indica	2759	91.30%	8.60%	0.04%	0.00%	NA
All Japonica	1512	89.90%	10.10%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	97.80%	2.20%	0.00%	0.00%	NA
Indica II	465	95.10%	4.90%	0.00%	0.00%	NA
Indica III	913	84.60%	15.30%	0.11%	0.00%	NA
Indica Intermediate	786	92.10%	7.90%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	73.20%	26.80%	0.00%	0.00%	NA
Japonica Intermediate	241	93.40%	6.60%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0812056816	C -> T	LOC_Os08g20110.1	missense_variant ; p.Thr976Ile; MODERATE	nonsynonymous_codon ; T976I	Average:51.426; most accessible tissue: Zhenshan97 flag leaf, score: 73.822	unknown	unknown	DELETERIOUS	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0812056816	NA	9.03E-06	mr1134	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
vg0812056816	NA	1.15E-06	mr1583	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
vg0812056816	5.20E-07	8.05E-07	mr1835	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