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Detailed information for vg1209004478:

Variant ID: vg1209004478 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9004478
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.64, C: 0.36, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

AGGCGAAGAAACCGGTCGGCAGTGATGACGGCGGCCAGCGATGAAGGTGTAGATGCCCAACAACGGTGGTGTGACCAACCAACCGTGTAGGCGAGGACAC[T/C]
AGTTGACAGTGGACGAGGCGGCCGGTCAGTGAAGACGATGATGTCCATCAGCAGCGGCGCAATATGCCAGCCGTGAAGGCGAAGAGGCTTGTCGACGGAA

Reverse complement sequence

TTCCGTCGACAAGCCTCTTCGCCTTCACGGCTGGCATATTGCGCCGCTGCTGATGGACATCATCGTCTTCACTGACCGGCCGCCTCGTCCACTGTCAACT[A/G]
GTGTCCTCGCCTACACGGTTGGTTGGTCACACCACCGTTGTTGGGCATCTACACCTTCATCGCTGGCCGCCGTCATCACTGCCGACCGGTTTCTTCGCCT

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	39.80%	37.90%	0.59%	21.71%	NA
All Indica	2759	54.10%	10.10%	0.98%	34.83%	NA
All Japonica	1512	4.40%	94.50%	0.00%	1.06%	NA
Aus	269	81.00%	5.20%	0.37%	13.38%	NA
Indica I	595	36.50%	20.50%	1.01%	42.02%	NA
Indica II	465	51.80%	11.80%	1.08%	35.27%	NA
Indica III	913	65.20%	2.60%	0.55%	31.65%	NA
Indica Intermediate	786	56.00%	9.80%	1.40%	32.82%	NA
Temperate Japonica	767	6.00%	93.00%	0.00%	1.04%	NA
Tropical Japonica	504	3.60%	95.60%	0.00%	0.79%	NA
Japonica Intermediate	241	1.20%	97.10%	0.00%	1.66%	NA
VI/Aromatic	96	72.90%	22.90%	0.00%	4.17%	NA
Intermediate	90	37.80%	52.20%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209004478	T -> C	LOC_Os12g15770.1	missense_variant ; p.Ser54Gly; MODERATE	nonsynonymous_codon ; S54G	Average:44.259; most accessible tissue: Callus, score: 82.589	unknown	unknown	TOLERATED	1.00
vg1209004478	T -> DEL	LOC_Os12g15770.1	N	frameshift_variant	Average:44.259; most accessible tissue: Callus, score: 82.589	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209004478	NA	1.47E-07	mr1425	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
vg1209004478	NA	8.41E-06	mr1864_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