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Detailed information for vg0428807864:

Variant ID: vg0428807864 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 28807864
Reference Allele: ACCACC	Alternative Allele: A
Primary Allele: ACCACC	Secondary Allele: Unkown

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGACTAGGAATTGCTTAGCCATGCTTAGTTCCACTAGCACACATTGGGGAAAGCTCACTAAAATATAGCCTTTAGGTTCAATTGGTAAGGTTGGTTTAGT[ACCACC/A]
GTTTTGGTGTTGGTTAATTAAAATGAATCACATGGTGGGCTGTGGGTGCATGGTTTTGCTGGTCGCACCCATGGCATTTAAGGACCGGTTCGCGGGATGC

Reverse complement sequence

GCATCCCGCGAACCGGTCCTTAAATGCCATGGGTGCGACCAGCAAAACCATGCACCCACAGCCCACCATGTGATTCATTTTAATTAACCAACACCAAAAC[GGTGGT/T]
ACTAAACCAACCTTACCAATTGAACCTAAAGGCTATATTTTAGTGAGCTTTCCCCAATGTGTGCTAGTGGAACTAAGCATGGCTAAGCAATTCCTAGTCC

Allele Frequencies:

Populations	Population Size	Frequency of ACCACC(primary allele)	Frequency of Unkown(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.80%	0.00%	0.19%	0.02%	NA
All Indica	2759	99.60%	0.00%	0.33%	0.04%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.70%	0.00%	1.18%	0.17%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.80%	0.00%	0.22%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0428807864	ACCACC -> A	LOC_Os04g48320.1	downstream_gene_variant ; 1039.0bp to feature; MODIFIER	N	Average:27.002; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N
vg0428807864	ACCACC -> A	LOC_Os04g48310-LOC_Os04g48320	intergenic_region ; MODIFIER	N	Average:27.002; most accessible tissue: Minghui63 panicle, score: 68.46	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0428807864	4.65E-06	4.05E-06	mr1127	Ind_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