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Detailed information for vg0811676655:

Variant ID: vg0811676655 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 11676655
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

TCCTGAGAGTCAGCTGGCAGAGTATCAGGACTAACCATTCTGTCCTTTCCACACTTGAGTAGATTTTTCAGATAGTTCACTCTTGGGCGTTTAGGATCAG[G/C]
ATCAACAGCCCTTGTCTTGTACAGCCTCAAAGGATTGCTTTCAGAACCAGGCTCATCCTCATTGCCACCATCATCTGACTCAGATGCAGCTGGAGAGGGA

Reverse complement sequence

TCCCTCTCCAGCTGCATCTGAGTCAGATGATGGTGGCAATGAGGATGAGCCTGGTTCTGAAAGCAATCCTTTGAGGCTGTACAAGACAAGGGCTGTTGAT[C/G]
CTGATCCTAAACGCCCAAGAGTGAACTATCTGAAAAATCTACTCAAGTGTGGAAAGGACAGAATGGTTAGTCCTGATACTCTGCCAGCTGACTCTCAGGA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.30%	3.70%	0.99%	15.07%	NA
All Indica	2759	92.40%	0.30%	0.07%	7.18%	NA
All Japonica	1512	58.80%	10.10%	1.52%	29.63%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.20%	0.00%	0.00%	1.85%	NA
Indica II	465	95.70%	0.00%	0.22%	4.09%	NA
Indica III	913	86.60%	0.40%	0.11%	12.81%	NA
Indica Intermediate	786	92.90%	0.60%	0.00%	6.49%	NA
Temperate Japonica	767	90.20%	0.30%	0.26%	9.26%	NA
Tropical Japonica	504	18.80%	26.60%	2.38%	52.18%	NA
Japonica Intermediate	241	42.30%	6.60%	3.73%	47.30%	NA
VI/Aromatic	96	17.70%	7.30%	18.75%	56.25%	NA
Intermediate	90	76.70%	5.60%	4.44%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0811676655	G -> C	LOC_Os08g19530.1	missense_variant ; p.Pro331Ala; MODERATE	nonsynonymous_codon ; P331A	Average:40.303; most accessible tissue: Zhenshan97 flag leaf, score: 58.772	unknown	unknown	DELETERIOUS	0.02
vg0811676655	G -> DEL	LOC_Os08g19530.1	N	frameshift_variant	Average:40.303; most accessible tissue: Zhenshan97 flag leaf, score: 58.772	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0811676655	NA	2.25E-07	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
vg0811676655	NA	4.61E-07	mr1135	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
vg0811676655	7.80E-07	2.36E-08	mr1504	Jap_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
vg0811676655	NA	7.69E-08	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
vg0811676655	NA	8.03E-07	mr1188_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