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Detailed information for vg1223152520:

Variant ID: vg1223152520 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23152520
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCACTGGGCCACACAAGTCCCCGTGCACGAGCTCGAGCCGCTCCTTGGCTCGGAAGCTCGTCTGCTGGGGAAAGGGGAGCCGCCGCTGCTTCGTCACCAC[A/G]
CAGACGTCGCAGAGCTACTCCACGTGGTCAAGGCACGGCATGCCTCGCACCATCTCCTTGGCACTGAGGCGCTTCAGGGCCTCGAAGTGGAGGTGCCCGA

Reverse complement sequence

TCGGGCACCTCCACTTCGAGGCCCTGAAGCGCCTCAGTGCCAAGGAGATGGTGCGAGGCATGCCGTGCCTTGACCACGTGGAGTAGCTCTGCGACGTCTG[T/C]
GTGGTGACGAAGCAGCGGCGGCTCCCCTTTCCCCAGCAGACGAGCTTCCGAGCCAAGGAGCGGCTCGAGCTCGTGCACGGGGACTTGTGTGGCCCAGTGA

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	63.90%	17.80%	14.39%	3.91%	NA
All Indica	2759	75.70%	3.00%	15.19%	6.13%	NA
All Japonica	1512	45.80%	48.50%	5.09%	0.60%	NA
Aus	269	40.10%	1.10%	56.88%	1.86%	NA
Indica I	595	66.10%	5.40%	17.98%	10.59%	NA
Indica II	465	55.90%	4.10%	24.30%	15.70%	NA
Indica III	913	91.80%	0.70%	7.12%	0.44%	NA
Indica Intermediate	786	76.00%	3.30%	17.05%	3.69%	NA
Temperate Japonica	767	9.40%	83.60%	5.87%	1.17%	NA
Tropical Japonica	504	91.30%	5.60%	3.17%	0.00%	NA
Japonica Intermediate	241	66.80%	26.60%	6.64%	0.00%	NA
VI/Aromatic	96	87.50%	0.00%	12.50%	0.00%	NA
Intermediate	90	52.20%	24.40%	21.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1223152520	A -> DEL	N	N	silent_mutation	Average:53.173; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N
vg1223152520	A -> G	LOC_Os12g37720.1	downstream_gene_variant ; 4164.0bp to feature; MODIFIER	silent_mutation	Average:53.173; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N
vg1223152520	A -> G	LOC_Os12g37710.1	intron_variant ; MODIFIER	silent_mutation	Average:53.173; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N
vg1223152520	A -> G	LOC_Os12g37710.2	intron_variant ; MODIFIER	silent_mutation	Average:53.173; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223152520	6.95E-06	NA	mr1518	Jap_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