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Detailed information for vg0318829113:

Variant ID: vg0318829113 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 18829113
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.73, C: 0.27, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

ATGGCACGGGGACATGGTCCGAGTCGAGGAGAGAGATCTTGCTAAGGTCGTTGGTGATGAAGTTGAAACTGCCGAACCGGAACGCCTGCCCGGGAGGGAA[C/G]
GCGAAGTCGTCGATGCCAGAAACGAAACCCATCGCACTTAGTCGGTGAGAACTTGACGCTACCCCTACCTGGCGCACCAACTGTCGAAACAAGATTTCGA

Reverse complement sequence

TCGAAATCTTGTTTCGACAGTTGGTGCGCCAGGTAGGGGTAGCGTCAAGTTCTCACCGACTAAGTGCGATGGGTTTCGTTTCTGGCATCGACGACTTCGC[G/C]
TTCCCTCCCGGGCAGGCGTTCCGGTTCGGCAGTTTCAACTTCATCACCAACGACCTTAGCAAGATCTCTCTCCTCGACTCGGACCATGTCCCCGTGCCAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.40%	32.90%	0.95%	19.76%	NA
All Indica	2759	69.20%	4.00%	1.41%	25.41%	NA
All Japonica	1512	12.60%	85.70%	0.13%	1.59%	NA
Aus	269	21.60%	12.30%	0.74%	65.43%	NA
Indica I	595	58.00%	4.90%	1.18%	35.97%	NA
Indica II	465	41.50%	4.70%	3.87%	49.89%	NA
Indica III	913	91.90%	1.30%	0.33%	6.46%	NA
Indica Intermediate	786	67.60%	6.10%	1.40%	24.94%	NA
Temperate Japonica	767	0.30%	99.60%	0.13%	0.00%	NA
Tropical Japonica	504	33.90%	65.50%	0.20%	0.40%	NA
Japonica Intermediate	241	7.10%	83.80%	0.00%	9.13%	NA
VI/Aromatic	96	4.20%	71.90%	1.04%	22.92%	NA
Intermediate	90	35.60%	51.10%	1.11%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0318829113	C -> DEL	LOC_Os03g32930.1	N	frameshift_variant	Average:33.387; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N
vg0318829113	C -> G	LOC_Os03g32930.1	synonymous_variant ; p.Ala313Ala; LOW	synonymous_codon	Average:33.387; most accessible tissue: Minghui63 young leaf, score: 61.887	N	N	N	N
vg0318829113	C -> G	LOC_Os03g32930.1	synonymous_variant ; p.Ala313Ala; LOW	nonsynonymous_codon ; A313T	Average:33.387; most accessible tissue: Minghui63 young leaf, score: 61.887	benign	0.381	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0318829113	NA	3.38E-07	mr1136	Jap_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
vg0318829113	NA	1.48E-07	mr1217	Jap_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
vg0318829113	NA	2.41E-06	mr1830	Jap_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
vg0318829113	NA	4.09E-07	mr1845	Jap_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
vg0318829113	NA	7.10E-08	mr1852	Jap_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
vg0318829113	NA	4.05E-07	mr1045_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
vg0318829113	NA	1.76E-08	mr1136_2	Jap_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
vg0318829113	NA	7.97E-07	mr1252_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
vg0318829113	NA	5.39E-06	mr1391_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
vg0318829113	NA	2.99E-06	mr1505_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
vg0318829113	NA	9.02E-09	mr1612_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
vg0318829113	NA	3.82E-06	mr1763_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
vg0318829113	NA	5.75E-06	mr1771_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
vg0318829113	NA	5.62E-08	mr1783_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
vg0318829113	5.96E-06	NA	mr1784_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
vg0318829113	NA	6.31E-09	mr1785_2	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
vg0318829113	NA	4.08E-09	mr1804_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
vg0318829113	NA	1.84E-08	mr1837_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
vg0318829113	NA	3.29E-11	mr1844_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
vg0318829113	NA	3.81E-09	mr1947_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