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Detailed information for vg1204378188:

Variant ID: vg1204378188 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4378188
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.03, others allele: 0.00, population size: 36. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCGCAGCTCCTGCAGCTCCAGCTCCAGTCCCAGCTCCTGTCCCAGTGTCAGCTCCCGCGTCCGCTCTCTCCTTCGCTCCAGCATTAGCCGCCAGGGGT[C/T]
CAGCCAGTGGCAACGGGGGTTGGTTGCCTGCTACTCCCAGTGGCAGCCGCGACCACAGCAGCAGCAGTTCCAGTGGCTCGGAGCCGGGCAGCGGCGAGAT

Reverse complement sequence

ATCTCGCCGCTGCCCGGCTCCGAGCCACTGGAACTGCTGCTGCTGTGGTCGCGGCTGCCACTGGGAGTAGCAGGCAACCAACCCCCGTTGCCACTGGCTG[G/A]
ACCCCTGGCGGCTAATGCTGGAGCGAAGGAGAGAGCGGACGCGGGAGCTGACACTGGGACAGGAGCTGGGACTGGAGCTGGAGCTGCAGGAGCTGCGGGA

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	36.00%	4.10%	30.03%	29.86%	NA
All Indica	2759	25.00%	5.90%	35.77%	33.27%	NA
All Japonica	1512	56.30%	1.10%	19.51%	23.02%	NA
Aus	269	37.20%	3.00%	40.89%	18.96%	NA
Indica I	595	44.20%	4.40%	27.56%	23.87%	NA
Indica II	465	30.30%	6.50%	25.81%	37.42%	NA
Indica III	913	5.90%	6.80%	49.40%	37.90%	NA
Indica Intermediate	786	29.60%	5.70%	32.06%	32.57%	NA
Temperate Japonica	767	80.60%	0.10%	6.65%	12.65%	NA
Tropical Japonica	504	29.80%	2.60%	41.47%	26.19%	NA
Japonica Intermediate	241	34.90%	1.20%	14.52%	49.38%	NA
VI/Aromatic	96	15.60%	2.10%	13.54%	68.75%	NA
Intermediate	90	48.90%	4.40%	15.56%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204378188	C -> DEL	LOC_Os12g08610.1	N	frameshift_variant	Average:12.871; most accessible tissue: Callus, score: 35.2	N	N	N	N
vg1204378188	C -> T	LOC_Os12g08610.1	missense_variant ; p.Ser309Phe; MODERATE	nonsynonymous_codon ; S309F	Average:12.871; most accessible tissue: Callus, score: 35.2	unknown	unknown	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204378188	3.97E-06	NA	mr1169	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