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Detailed information for vg1200546779:

Variant ID: vg1200546779 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 546779
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

ACAATTTGCGGACCGCATGATTCTCTCAGCAAGTAAGAAGTTGCGAAAGAGACTAGCAACCAAAAGATCCTGCCTGAAAAGTCTTTGGAATAGATCTGCG[C/T]
AGTGAAAGTTGAATCATAACAGATTAAAAGAAAATGAATGAGAAAGCAATTGATCACTGGCATTAATTGTAACTAAAACGACTATCAGTACCATGAGGAA

Reverse complement sequence

TTCCTCATGGTACTGATAGTCGTTTTAGTTACAATTAATGCCAGTGATCAATTGCTTTCTCATTCATTTTCTTTTAATCTGTTATGATTCAACTTTCACT[G/A]
CGCAGATCTATTCCAAAGACTTTTCAGGCAGGATCTTTTGGTTGCTAGTCTCTTTCGCAACTTCTTACTTGCTGAGAGAATCATGCGGTCCGCAAATTGT

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	37.20%	9.90%	48.20%	4.76%	NA
All Indica	2759	3.50%	15.90%	73.29%	7.25%	NA
All Japonica	1512	95.70%	0.50%	3.24%	0.60%	NA
Aus	269	24.50%	5.20%	65.06%	5.20%	NA
Indica I	595	2.20%	14.10%	77.14%	6.55%	NA
Indica II	465	3.70%	9.70%	73.98%	12.69%	NA
Indica III	913	3.50%	19.50%	71.96%	5.04%	NA
Indica Intermediate	786	4.50%	16.90%	71.50%	7.12%	NA
Temperate Japonica	767	93.90%	0.70%	4.82%	0.65%	NA
Tropical Japonica	504	97.40%	0.20%	1.79%	0.60%	NA
Japonica Intermediate	241	97.90%	0.40%	1.24%	0.41%	NA
VI/Aromatic	96	92.70%	0.00%	7.29%	0.00%	NA
Intermediate	90	64.40%	5.60%	27.78%	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
vg1200546779	C -> DEL	N	N	silent_mutation	Average:29.008; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N
vg1200546779	C -> T	LOC_Os12g01922.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:29.008; most accessible tissue: Minghui63 young leaf, score: 42.042	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200546779	6.67E-06	NA	mr1120	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
vg1200546779	NA	1.31E-16	mr1164	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
vg1200546779	NA	5.35E-28	mr1298	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
vg1200546779	NA	7.45E-15	mr1361	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
vg1200546779	NA	3.35E-06	mr1508	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
vg1200546779	NA	1.27E-23	mr1571	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
vg1200546779	NA	1.60E-19	mr1627	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
vg1200546779	NA	1.27E-08	mr1776	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
vg1200546779	1.28E-06	NA	mr1858	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
vg1200546779	1.24E-06	NA	mr1859	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