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Detailed information for vg1224506348:

Variant ID: vg1224506348 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24506348
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

ACGAATGGCGGCGGCAACGTGTCGGCGGTCAGGGACCCCGACATGTGGCGTGACGGCCTCCGCATTGCCTCGGCCGTGAGGCCCTCCCCCGTGGCGTCGA[G/A]
CCGCCGACTACTTCGATCTTGGTTGGTCCATTCTTGTTAAATCCAAACAGATGTTGTCCCTAGATTGGATGAGTTCATTTGTCAAATTGACAGTGAGAAA

Reverse complement sequence

TTTCTCACTGTCAATTTGACAAATGAACTCATCCAATCTAGGGACAACATCTGTTTGGATTTAACAAGAATGGACCAACCAAGATCGAAGTAGTCGGCGG[C/T]
TCGACGCCACGGGGGAGGGCCTCACGGCCGAGGCAATGCGGAGGCCGTCACGCCACATGTCGGGGTCCCTGACCGCCGACACGTTGCCGCCGCCATTCGT

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	72.10%	13.40%	2.16%	12.31%	NA
All Indica	2759	87.00%	1.30%	0.47%	11.20%	NA
All Japonica	1512	60.10%	34.90%	4.96%	0.07%	NA
Aus	269	3.70%	0.40%	1.86%	94.05%	NA
Indica I	595	63.40%	0.00%	1.34%	35.29%	NA
Indica II	465	95.50%	3.20%	0.00%	1.29%	NA
Indica III	913	97.30%	0.80%	0.00%	1.97%	NA
Indica Intermediate	786	88.00%	1.80%	0.64%	9.54%	NA
Temperate Japonica	767	74.20%	19.00%	6.78%	0.00%	NA
Tropical Japonica	504	35.90%	60.90%	3.17%	0.00%	NA
Japonica Intermediate	241	66.00%	30.70%	2.90%	0.41%	NA
VI/Aromatic	96	29.20%	58.30%	2.08%	10.42%	NA
Intermediate	90	65.60%	16.70%	7.78%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1224506348	G -> DEL	LOC_Os12g39690.1	N	frameshift_variant	Average:40.114; most accessible tissue: Minghui63 panicle, score: 78.92	N	N	N	N
vg1224506348	G -> A	LOC_Os12g39690.1	missense_variant ; p.Ser20Asn; MODERATE	nonsynonymous_codon ; S20N	Average:40.114; most accessible tissue: Minghui63 panicle, score: 78.92	unknown	unknown	DELETERIOUS	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224506348	8.39E-06	5.39E-08	mr1888	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