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Detailed information for vg1224302733:

Variant ID: vg1224302733 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24302733
Reference Allele: C	Alternative Allele: T,G
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

ACTCCAGGTCTACAGCCAGTGTGCCTCGATCTACTCTCTGTACGCATAGTAAATTGTTGGCTTAGGAGGCATCAGGAGCTCCGGTAACACCATAGTGTGC[C/T,G]
TCGATCTACTCTCTACGCATAGTAAATTGAGCTTGTGTCGCTACAACCGTAGCCACGGAGCTAGAACTTGCTTCCAACCTGATGAGCAACAATGTCGGCC

Reverse complement sequence

GGCCGACATTGTTGCTCATCAGGTTGGAAGCAAGTTCTAGCTCCGTGGCTACGGTTGTAGCGACACAAGCTCAATTTACTATGCGTAGAGAGTAGATCGA[G/A,C]
GCACACTATGGTGTTACCGGAGCTCCTGATGCCTCCTAAGCCAACAATTTACTATGCGTACAGAGAGTAGATCGAGGCACACTGGCTGTAGACCTGGAGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.00%	1.50%	1.40%	22.03%	G: 0.02%
All Indica	2759	60.20%	0.70%	2.21%	36.97%	NA
All Japonica	1512	95.90%	3.40%	0.26%	0.46%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	71.10%	0.00%	1.85%	27.06%	NA
Indica II	465	50.30%	2.20%	2.80%	44.73%	NA
Indica III	913	67.60%	0.00%	1.42%	31.00%	NA
Indica Intermediate	786	49.10%	1.00%	3.05%	46.82%	NA
Temperate Japonica	767	98.80%	0.30%	0.00%	0.91%	NA
Tropical Japonica	504	90.10%	9.30%	0.60%	0.00%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	0.00%	G: 1.04%
Intermediate	90	82.20%	3.30%	1.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1224302733	C -> DEL	N	N	silent_mutation	Average:61.253; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg1224302733	C -> G	LOC_Os12g39440-LOC_Os12g39450	intergenic_region ; MODIFIER	silent_mutation	Average:61.253; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N
vg1224302733	C -> T	LOC_Os12g39440-LOC_Os12g39450	intergenic_region ; MODIFIER	silent_mutation	Average:61.253; most accessible tissue: Zhenshan97 young leaf, score: 79.783	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224302733	9.19E-07	1.48E-07	mr1794	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
vg1224302733	9.67E-06	3.15E-08	mr1800_2	Jap_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