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Detailed information for vg1213914348:

Variant ID: vg1213914348 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 13914348
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

CCGTGGTGGACGTGAGCGGCAGCATGCGAGGGCACAAGATCGAGAGCGTCAAGAAGGCCCTGCAGTTCGTGATCATGAAGCTTACCCCCGTGGACCGCCT[C/T]
TCCATCGTCACCTTCGAAAGCAGCGCCAAGAGACTCACCAAGCTTCGTGCCATGACCCAGGACTTCCGGGGCGAGCTCGACGGAATCGTCAAATCCCTCA

Reverse complement sequence

TGAGGGATTTGACGATTCCGTCGAGCTCGCCCCGGAAGTCCTGGGTCATGGCACGAAGCTTGGTGAGTCTCTTGGCGCTGCTTTCGAAGGTGACGATGGA[G/A]
AGGCGGTCCACGGGGGTAAGCTTCATGATCACGAACTGCAGGGCCTTCTTGACGCTCTCGATCTTGTGCCCTCGCATGCTGCCGCTCACGTCCACCACGG

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	87.00%	12.70%	0.17%	0.11%	NA
All Indica	2759	79.50%	20.10%	0.22%	0.18%	NA
All Japonica	1512	97.10%	2.80%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.00%	2.00%	0.00%	0.00%	NA
Indica II	465	53.10%	45.80%	0.65%	0.43%	NA
Indica III	913	82.30%	17.20%	0.33%	0.22%	NA
Indica Intermediate	786	78.00%	21.90%	0.00%	0.13%	NA
Temperate Japonica	767	94.80%	5.20%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1213914348	C -> DEL	LOC_Os12g24390.1	N	frameshift_variant	Average:76.36; most accessible tissue: Zhenshan97 young leaf, score: 91.967	N	N	N	N
vg1213914348	C -> T	LOC_Os12g24390.1	synonymous_variant ; p.Leu98Leu; LOW	synonymous_codon	Average:76.36; most accessible tissue: Zhenshan97 young leaf, score: 91.967	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1213914348	NA	1.93E-06	mr1024_2	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