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Detailed information for vg0512420077:

Variant ID: vg0512420077 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 12420077
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

GCTAGTTACCCCTTCAGGGTTTCTCGGGTTTTGATGATAGAGATAGCTTCTTGCTACCGGCTCGCAGCGCGCGTGTTGGCTAAACCGCCCGTCTGCATGT[A/C]
ATCGGAACCCCACCATATTGTGTTTGATAGTGAAACTTTCATCTTTATCTAGCAATCTCAGTGCTTGTCCTACTTGTTCTTGCTTGTTCTTCGATTGCTT

Reverse complement sequence

AAGCAATCGAAGAACAAGCAAGAACAAGTAGGACAAGCACTGAGATTGCTAGATAAAGATGAAAGTTTCACTATCAAACACAATATGGTGGGGTTCCGAT[T/G]
ACATGCAGACGGGCGGTTTAGCCAACACGCGCGCTGCGAGCCGGTAGCAAGAAGCTATCTCTATCATCAAAACCCGAGAAACCCTGAAGGGGTAACTAGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.70%	2.50%	4.68%	8.17%	NA
All Indica	2759	81.90%	4.10%	5.18%	8.74%	NA
All Japonica	1512	99.60%	0.10%	0.07%	0.26%	NA
Aus	269	23.00%	0.00%	27.51%	49.44%	NA
Indica I	595	91.60%	0.00%	2.02%	6.39%	NA
Indica II	465	74.80%	21.70%	2.58%	0.86%	NA
Indica III	913	77.00%	0.10%	9.31%	13.58%	NA
Indica Intermediate	786	84.60%	1.50%	4.33%	9.54%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.00%	0.20%	0.60%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	87.80%	1.10%	3.33%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0512420077	A -> DEL	N	N	silent_mutation	Average:47.242; most accessible tissue: Zhenshan97 flag leaf, score: 73.475	N	N	N	N
vg0512420077	A -> C	LOC_Os05g21120.1	intron_variant ; MODIFIER	silent_mutation	Average:47.242; most accessible tissue: Zhenshan97 flag leaf, score: 73.475	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0512420077	NA	2.78E-33	mr1039	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
vg0512420077	NA	2.65E-19	mr1039	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
vg0512420077	NA	8.43E-09	mr1632	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
vg0512420077	1.49E-15	1.94E-39	mr1039_2	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
vg0512420077	4.98E-11	3.55E-23	mr1039_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
vg0512420077	7.88E-07	NA	mr1514_2	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
vg0512420077	4.60E-06	NA	mr1514_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
vg0512420077	9.35E-18	NA	mr1632_2	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
vg0512420077	5.67E-15	1.85E-19	mr1632_2	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