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Detailed information for vg1111075762:

Variant ID: vg1111075762 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 11075762
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

GCCGACGCGTCCCCATCCAACTGTTGTATCTCTCCCTCCTACCGTTGATGAAAGAGATAAAGATCTCCAATTACAGTATGATATAGATTTAGAGGACGAC[G/A]
GTATGAAGGTCGACAGCAGGCCGCACCTCCCCCCTCCTGCCAAAAGGAGCAAGAGGGCGAAATCTTCTCCACCTAAACTTGACACACGCAGAAAAGCTGC

Reverse complement sequence

GCAGCTTTTCTGCGTGTGTCAAGTTTAGGTGGAGAAGATTTCGCCCTCTTGCTCCTTTTGGCAGGAGGGGGGAGGTGCGGCCTGCTGTCGACCTTCATAC[C/T]
GTCGTCCTCTAAATCTATATCATACTGTAATTGGAGATCTTTATCTCTTTCATCAACGGTAGGAGGGAGAGATACAACAGTTGGATGGGGACGCGTCGGC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.10%	41.20%	0.53%	2.18%	NA
All Indica	2759	34.80%	60.70%	0.83%	3.66%	NA
All Japonica	1512	96.60%	3.20%	0.13%	0.07%	NA
Aus	269	29.70%	70.30%	0.00%	0.00%	NA
Indica I	595	8.90%	88.90%	0.84%	1.34%	NA
Indica II	465	61.30%	33.80%	1.08%	3.87%	NA
Indica III	913	30.30%	63.60%	0.88%	5.15%	NA
Indica Intermediate	786	44.00%	51.80%	0.64%	3.56%	NA
Temperate Japonica	767	98.70%	1.30%	0.00%	0.00%	NA
Tropical Japonica	504	92.70%	6.70%	0.40%	0.20%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	91.70%	8.30%	0.00%	0.00%	NA
Intermediate	90	68.90%	30.00%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1111075762	G -> A	LOC_Os11g19330.1	missense_variant ; p.Gly365Ser; MODERATE	nonsynonymous_codon ; G365R	Average:59.005; most accessible tissue: Minghui63 flag leaf, score: 71.116	probably damaging	2.607	TOLERATED	0.96
vg1111075762	G -> A	LOC_Os11g19330.1	missense_variant ; p.Gly365Ser; MODERATE	nonsynonymous_codon ; G365S	Average:59.005; most accessible tissue: Minghui63 flag leaf, score: 71.116	possibly damaging	1.834	TOLERATED	0.63
vg1111075762	G -> DEL	LOC_Os11g19330.1	N	frameshift_variant	Average:59.005; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1111075762	NA	2.06E-11	mr1277	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
vg1111075762	4.13E-07	NA	mr1758	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
vg1111075762	6.87E-06	1.23E-07	mr1758	Ind_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
vg1111075762	NA	4.50E-08	mr1829	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
vg1111075762	NA	1.55E-12	mr1902	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
vg1111075762	NA	2.16E-07	mr1154_2	Ind_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