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Detailed information for vg1120091074:

Variant ID: vg1120091074 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 20091074
Reference Allele: G	Alternative Allele: A,GCA
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAATTAGTTATGATTTTTAGAAGATTCTCTGTGTTTTTACTATAAAAGAAAAACCCTTAATCAATTTATTGCGCAATAATTCATCCCAGGGCTGACGTCA[G/A,GCA]
CAAGGGGTGGGGCGGCGCCGACATGCGGGCCCCACTGGTCAGCGGCACTAAGAGAGGGAGAAAGGGGGCAGCTGGCAGGCGGTCCCACCGGGCAGCGTCA

Reverse complement sequence

TGACGCTGCCCGGTGGGACCGCCTGCCAGCTGCCCCCTTTCTCCCTCTCTTAGTGCCGCTGACCAGTGGGGCCCGCATGTCGGCGCCGCCCCACCCCTTG[C/T,TGC]
TGACGTCAGCCCTGGGATGAATTATTGCGCAATAAATTGATTAAGGGTTTTTCTTTTATAGTAAAAACACAGAGAATCTTCTAAAAATCATAACTAATTC

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	93.30%	6.70%	0.02%	0.00%	GCA: 0.02%
All Indica	2759	99.70%	0.20%	0.04%	0.00%	NA
All Japonica	1512	79.60%	20.40%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.10%	0.11%	0.00%	NA
Indica Intermediate	786	99.50%	0.50%	0.00%	0.00%	NA
Temperate Japonica	767	81.70%	18.30%	0.00%	0.00%	NA
Tropical Japonica	504	69.20%	30.80%	0.00%	0.00%	NA
Japonica Intermediate	241	94.60%	5.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	0.00%	0.00%	GCA: 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
vg1120091074	G -> GCA	LOC_Os11g34290.1	intron_variant ; MODIFIER	silent_mutation	Average:65.624; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N
vg1120091074	G -> A	LOC_Os11g34290.1	intron_variant ; MODIFIER	silent_mutation	Average:65.624; most accessible tissue: Minghui63 panicle, score: 80.641	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1120091074	4.18E-06	NA	mr1115	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