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Detailed information for vg1126836664:

Variant ID: vg1126836664 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26836664
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAAATAACAAAGAAATAGGAGCCAGAGAAAGAGAAGGTATGACATAGACGAGAGAAATAGATATATTTGATGGCTGGTCCATTTGTTCAATTACCTCGG[A/C]
TAACTCTTTGTACTCTACTTCTGCTATAAGCGATAGAAATTTCCACATTAAACCAAAAAAATAATTGTTCAAGTAAAAATACAATTTAAAAGTAACTAAA

Reverse complement sequence

TTTAGTTACTTTTAAATTGTATTTTTACTTGAACAATTATTTTTTTGGTTTAATGTGGAAATTTCTATCGCTTATAGCAGAAGTAGAGTACAAAGAGTTA[T/G]
CCGAGGTAATTGAACAAATGGACCAGCCATCAAATATATCTATTTCTCTCGTCTATGTCATACCTTCTCTTTCTCTGGCTCCTATTTCTTTGTTATTTTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.10%	8.50%	4.25%	11.17%	NA
All Indica	2759	67.90%	10.40%	5.55%	16.20%	NA
All Japonica	1512	90.60%	4.60%	1.39%	3.44%	NA
Aus	269	70.30%	13.00%	8.55%	8.18%	NA
Indica I	595	93.30%	1.80%	2.86%	2.02%	NA
Indica II	465	57.60%	1.90%	1.72%	38.71%	NA
Indica III	913	60.60%	19.90%	10.62%	8.87%	NA
Indica Intermediate	786	63.20%	10.70%	3.94%	22.14%	NA
Temperate Japonica	767	95.70%	0.50%	0.26%	3.52%	NA
Tropical Japonica	504	82.90%	12.90%	1.39%	2.78%	NA
Japonica Intermediate	241	90.50%	0.00%	4.98%	4.56%	NA
VI/Aromatic	96	89.60%	9.40%	1.04%	0.00%	NA
Intermediate	90	85.60%	3.30%	3.33%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126836664	A -> DEL	N	N	silent_mutation	Average:44.248; most accessible tissue: Minghui63 root, score: 67.73	N	N	N	N
vg1126836664	A -> C	LOC_Os11g44380.1	upstream_gene_variant ; 3810.0bp to feature; MODIFIER	silent_mutation	Average:44.248; most accessible tissue: Minghui63 root, score: 67.73	N	N	N	N
vg1126836664	A -> C	LOC_Os11g44380-LOC_Os11g44390	intergenic_region ; MODIFIER	silent_mutation	Average:44.248; most accessible tissue: Minghui63 root, score: 67.73	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126836664	NA	8.78E-08	Grain_thickness	Ind_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