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Detailed information for vg1221303134:

Variant ID: vg1221303134 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21303134
Reference Allele: G	Alternative Allele: C
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, C: 0.02, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

CTCTAACAAACACCTTGCATGCATCGAACAGTGCACGGTGTGAGAAGGAAAAAGCAGAGCTCCTAAAACAGAGCTCCATAGTGCCAGCTTATATCATCAA[G/C]
TCTAACATTCTCCCCCTAAGCCTGGCACCGTGAACTGACCTCGACGACGCTGATGCGAGCTCGCAATTCTTGAAAACGAACCCGCCCGAGTGCCTTGGTC

Reverse complement sequence

GACCAAGGCACTCGGGCGGGTTCGTTTTCAAGAATTGCGAGCTCGCATCAGCGTCGTCGAGGTCAGTTCACGGTGCCAGGCTTAGGGGGAGAATGTTAGA[C/G]
TTGATGATATAAGCTGGCACTATGGAGCTCTGTTTTAGGAGCTCTGCTTTTTCCTTCTCACACCGTGCACTGTTCGATGCATGCAAGGTGTTTGTTAGAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.80%	6.70%	1.42%	8.08%	NA
All Indica	2759	76.20%	9.50%	2.07%	12.29%	NA
All Japonica	1512	99.50%	0.40%	0.07%	0.00%	NA
Aus	269	68.80%	14.50%	2.60%	14.13%	NA
Indica I	595	83.40%	8.40%	2.02%	6.22%	NA
Indica II	465	81.10%	9.00%	2.80%	7.10%	NA
Indica III	913	64.70%	12.70%	1.42%	21.14%	NA
Indica Intermediate	786	81.20%	6.70%	2.42%	9.67%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	4.20%	1.04%	0.00%	NA
Intermediate	90	86.70%	6.70%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1221303134	G -> C	LOC_Os12g35000.1	intron_variant ; MODIFIER	silent_mutation	Average:64.591; most accessible tissue: Zhenshan97 young leaf, score: 87.443	N	N	N	N
vg1221303134	G -> DEL	N	N	silent_mutation	Average:64.591; most accessible tissue: Zhenshan97 young leaf, score: 87.443	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221303134	NA	9.78E-06	mr1042	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
vg1221303134	2.82E-06	NA	mr1758	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