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Detailed information for vg1218428323:

Variant ID: vg1218428323 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18428323
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

CGAACGTACAAATGGCAAGATCCTAGAAGCACTAAAGAAAGGCAAATGGCCAGAAGAATTGCTATCGGTTCTCTGGGCCCTTCGGACGACCCCCACAAGA[C/A]
CAACCAAGTTTAGCCCGTTTATGCTTCTTTATGGCGATGAGGCAATGACCCCAGCAGAGCTAGGGGCTAACTCACCAAGGGTGATGTTCTCTGGGGGCGA

Reverse complement sequence

TCGCCCCCAGAGAACATCACCCTTGGTGAGTTAGCCCCTAGCTCTGCTGGGGTCATTGCCTCATCGCCATAAAGAAGCATAAACGGGCTAAACTTGGTTG[G/T]
TCTTGTGGGGGTCGTCCGAAGGGCCCAGAGAACCGATAGCAATTCTTCTGGCCATTTGCCTTTCTTTAGTGCTTCTAGGATCTTGCCATTTGTACGTTCG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.40%	19.20%	4.78%	3.68%	NA
All Indica	2759	53.40%	32.50%	7.94%	6.16%	NA
All Japonica	1512	99.60%	0.00%	0.26%	0.13%	NA
Aus	269	98.90%	0.40%	0.37%	0.37%	NA
Indica I	595	57.60%	22.20%	8.40%	11.76%	NA
Indica II	465	59.80%	19.40%	13.76%	7.10%	NA
Indica III	913	44.90%	46.30%	5.81%	2.96%	NA
Indica Intermediate	786	56.10%	32.20%	6.62%	5.09%	NA
Temperate Japonica	767	99.50%	0.00%	0.39%	0.13%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	6.70%	2.22%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1218428323	C -> DEL	LOC_Os12g30680.1	N	frameshift_variant	Average:36.354; most accessible tissue: Minghui63 young leaf, score: 54.11	N	N	N	N
vg1218428323	C -> A	LOC_Os12g30680.1	missense_variant ; p.Pro842Thr; MODERATE	nonsynonymous_codon ; P842T	Average:36.354; most accessible tissue: Minghui63 young leaf, score: 54.11	possibly damaging	1.787	TOLERATED	0.16

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218428323	2.58E-06	2.58E-06	mr1025	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
vg1218428323	NA	1.46E-06	mr1403	Ind_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