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Detailed information for vg1200180642:

Variant ID: vg1200180642 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 180642
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: 69. )

Flanking Sequence (100 bp) in Reference Genome:

GCACCAGCTACCCCAATCTCTTTGCTGTGACTATGTATATGTCTGATTCAGTCAAGGCCATGTGTTCAAGACCCTTAGAAGACTCTTTTGCACTACCCCT[C/A]
TCAGATGAGGCTTATTCGGAATTCTTGCAGCTTCAGGGGGTTCTGGACAGTTTGACTTTACAATCAGGGATGGGGGATGCTTGGAATTTTATCTGGGACT

Reverse complement sequence

AGTCCCAGATAAAATTCCAAGCATCCCCCATCCCTGATTGTAAAGTCAAACTGTCCAGAACCCCCTGAAGCTGCAAGAATTCCGAATAAGCCTCATCTGA[G/T]
AGGGGTAGTGCAAAAGAGTCTTCTAAGGGTCTTGAACACATGGCCTTGACTGAATCAGACATATACATAGTCACAGCAAAGAGATTGGGGTAGCTGGTGC

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	49.00%	19.10%	30.47%	1.40%	NA
All Indica	2759	19.90%	29.40%	49.22%	1.41%	NA
All Japonica	1512	96.90%	0.10%	1.46%	1.59%	NA
Aus	269	54.30%	31.20%	14.50%	0.00%	NA
Indica I	595	21.70%	21.70%	54.79%	1.85%	NA
Indica II	465	15.10%	18.50%	63.66%	2.80%	NA
Indica III	913	19.90%	44.00%	35.27%	0.77%	NA
Indica Intermediate	786	21.50%	24.80%	52.67%	1.02%	NA
Temperate Japonica	767	96.10%	0.10%	1.56%	2.22%	NA
Tropical Japonica	504	97.40%	0.00%	1.39%	1.19%	NA
Japonica Intermediate	241	98.30%	0.00%	1.24%	0.41%	NA
VI/Aromatic	96	95.80%	1.00%	2.08%	1.04%	NA
Intermediate	90	70.00%	6.70%	21.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1200180642	C -> DEL	LOC_Os12g01320.1	N	frameshift_variant	Average:15.386; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg1200180642	C -> A	LOC_Os12g01320.1	synonymous_variant ; p.Leu310Leu; LOW	synonymous_codon	Average:15.386; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200180642	NA	5.51E-10	mr1336	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
vg1200180642	2.25E-06	6.43E-08	mr1336	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
vg1200180642	NA	9.47E-08	mr1772	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