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Detailed information for vg1011831108:

Variant ID: vg1011831108 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 11831108
Reference Allele: C	Alternative Allele: G
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: 322. )

Flanking Sequence (100 bp) in Reference Genome:

CACCAACAGCAGGAAGAGAGGGAGCAGCAGCTGTGATGTTTCCACAGCTTCAAGTCCTGGAAAAAAAAAGCAAGAGCCCAGTGGTGAAGCTCATGAAGGG[C/G]
CTGCTCAATTCTTTCTCCTCTGAGAATGATAAGTCAACTACCCTCATTACTGAACTTGTTAACAACAAGAAGTTAAAGGACTAGAAGAAAGAAGACATGA

Reverse complement sequence

TCATGTCTTCTTTCTTCTAGTCCTTTAACTTCTTGTTGTTAACAAGTTCAGTAATGAGGGTAGTTGACTTATCATTCTCAGAGGAGAAAGAATTGAGCAG[G/C]
CCCTTCATGAGCTTCACCACTGGGCTCTTGCTTTTTTTTTCCAGGACTTGAAGCTGTGGAAACATCACAGCTGCTGCTCCCTCTCTTCCTGCTGTTGGTG

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	93.30%	6.10%	0.59%	0.00%	NA
All Indica	2759	99.70%	0.20%	0.07%	0.00%	NA
All Japonica	1512	80.00%	18.50%	1.52%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.20%	0.34%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	62.30%	34.90%	2.74%	0.00%	NA
Tropical Japonica	504	99.20%	0.60%	0.20%	0.00%	NA
Japonica Intermediate	241	95.90%	3.70%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	5.60%	3.33%	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
vg1011831108	C -> G	LOC_Os10g22760.1	missense_variant ; p.Pro277Ala; MODERATE	nonsynonymous_codon ; P277A	Average:37.239; most accessible tissue: Zhenshan97 young leaf, score: 76.099	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1011831108	6.69E-07	1.00E-09	Yield	Jap_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652