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Detailed information for vg1123286538:

Variant ID: vg1123286538 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 23286538
Reference Allele: GA	Alternative Allele: AA,G
Primary Allele: GA	Secondary Allele: AA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCTGCGCCGTCCGCGGTGCAGACGACGACGCGCACGGAAGAGGATTTTGATCCTCGAGGGAATATCCCCTCGTTGTTTGCATGTCAATTAAATGGTTAT[GA/AA,G]
AAAAATTTAAAAAAAATTAAGAAGATGTATTAATATGTGATATATCACTCCACAAACATGCAAGTAAAAATTTAACTTCTACATCTCGCAACGAAAAAAA

Reverse complement sequence

TTTTTTTCGTTGCGAGATGTAGAAGTTAAATTTTTACTTGCATGTTTGTGGAGTGATATATCACATATTAATACATCTTCTTAATTTTTTTTAAATTTTT[TC/TT,C]
ATAACCATTTAATTGACATGCAAACAACGAGGGGATATTCCCTCGAGGATCAAAATCCTCTTCCGTGCGCGTCGTCGTCTGCACCGCGGACGGCGCAGGT

Allele Frequencies:

Populations	Population Size	Frequency of GA(primary allele)	Frequency of AA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.30%	41.10%	0.53%	9.69%	G: 0.34%
All Indica	2759	31.20%	54.10%	0.69%	13.52%	G: 0.54%
All Japonica	1512	75.90%	23.10%	0.20%	0.73%	NA
Aus	269	82.20%	16.00%	0.00%	1.86%	NA
Indica I	595	59.50%	35.60%	0.17%	4.71%	NA
Indica II	465	5.60%	91.60%	0.43%	1.08%	G: 1.29%
Indica III	913	21.60%	45.60%	1.64%	30.56%	G: 0.66%
Indica Intermediate	786	36.00%	55.70%	0.13%	7.76%	G: 0.38%
Temperate Japonica	767	91.00%	8.50%	0.26%	0.26%	NA
Tropical Japonica	504	64.70%	34.90%	0.20%	0.20%	NA
Japonica Intermediate	241	51.50%	45.20%	0.00%	3.32%	NA
VI/Aromatic	96	12.50%	21.90%	1.04%	64.58%	NA
Intermediate	90	47.80%	41.10%	2.22%	7.78%	G: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123286538	GA -> AA	LOC_Os11g39120.1	upstream_gene_variant ; 1740.0bp to feature; MODIFIER	silent_mutation	Average:74.308; most accessible tissue: Zhenshan97 panicle, score: 92.133	N	N	N	N
vg1123286538	GA -> AA	LOC_Os11g39130.1	upstream_gene_variant ; 4516.0bp to feature; MODIFIER	silent_mutation	Average:74.308; most accessible tissue: Zhenshan97 panicle, score: 92.133	N	N	N	N
vg1123286538	GA -> AA	LOC_Os11g39130.3	upstream_gene_variant ; 4516.0bp to feature; MODIFIER	silent_mutation	Average:74.308; most accessible tissue: Zhenshan97 panicle, score: 92.133	N	N	N	N
vg1123286538	GA -> AA	LOC_Os11g39130.4	upstream_gene_variant ; 4516.0bp to feature; MODIFIER	silent_mutation	Average:74.308; most accessible tissue: Zhenshan97 panicle, score: 92.133	N	N	N	N
vg1123286538	GA -> AA	LOC_Os11g39120-LOC_Os11g39130	intergenic_region ; MODIFIER	silent_mutation	Average:74.308; most accessible tissue: Zhenshan97 panicle, score: 92.133	N	N	N	N
vg1123286538	GA -> DEL	N	N	silent_mutation	Average:74.308; most accessible tissue: Zhenshan97 panicle, score: 92.133	N	N	N	N
vg1123286538	GA -> G	LOC_Os11g39120.1	upstream_gene_variant ; 1741.0bp to feature; MODIFIER	silent_mutation	Average:74.308; most accessible tissue: Zhenshan97 panicle, score: 92.133	N	N	N	N
vg1123286538	GA -> G	LOC_Os11g39130.1	upstream_gene_variant ; 4515.0bp to feature; MODIFIER	silent_mutation	Average:74.308; most accessible tissue: Zhenshan97 panicle, score: 92.133	N	N	N	N
vg1123286538	GA -> G	LOC_Os11g39130.3	upstream_gene_variant ; 4515.0bp to feature; MODIFIER	silent_mutation	Average:74.308; most accessible tissue: Zhenshan97 panicle, score: 92.133	N	N	N	N
vg1123286538	GA -> G	LOC_Os11g39130.4	upstream_gene_variant ; 4515.0bp to feature; MODIFIER	silent_mutation	Average:74.308; most accessible tissue: Zhenshan97 panicle, score: 92.133	N	N	N	N
vg1123286538	GA -> G	LOC_Os11g39120-LOC_Os11g39130	intergenic_region ; MODIFIER	silent_mutation	Average:74.308; most accessible tissue: Zhenshan97 panicle, score: 92.133	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123286538	NA	2.16E-14	Grain_length	All	Not	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
vg1123286538	1.19E-06	6.16E-09	mr1312	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
vg1123286538	NA	6.97E-08	mr1347_2	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