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Detailed information for vg1218127576:

Variant ID: vg1218127576 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 18127576
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.64, C: 0.36, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

TGCAATTTCTGCCAGAACTTTGAAGTGAATTGGCTCCCTCGATCAGATACTATCTTTTTGGGTACTCCATGTAGACACATGATCCTCGAGAGATGGAGCT[A/C]
TGCCAACCTTTTGCCCGTATAAGTAGTATGCACTGGAATGAAATGAGCAACTTTGGTAAGTCGGTCCACGACTACCCAGATTGAATCGTGACCAGATGAT

Reverse complement sequence

ATCATCTGGTCACGATTCAATCTGGGTAGTCGTGGACCGACTTACCAAAGTTGCTCATTTCATTCCAGTGCATACTACTTATACGGGCAAAAGGTTGGCA[T/G]
AGCTCCATCTCTCGAGGATCATGTGTCTACATGGAGTACCCAAAAAGATAGTATCTGATCGAGGGAGCCAATTCACTTCAAAGTTCTGGCAGAAATTGCA

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	39.70%	36.70%	4.57%	19.04%	NA
All Indica	2759	9.40%	54.20%	7.72%	28.63%	NA
All Japonica	1512	90.80%	8.80%	0.07%	0.33%	NA
Aus	269	35.70%	30.90%	0.74%	32.71%	NA
Indica I	595	5.50%	87.10%	1.01%	6.39%	NA
Indica II	465	22.20%	33.10%	5.38%	39.35%	NA
Indica III	913	3.40%	48.10%	15.22%	33.30%	NA
Indica Intermediate	786	11.80%	49.00%	5.47%	33.72%	NA
Temperate Japonica	767	98.40%	0.90%	0.13%	0.52%	NA
Tropical Japonica	504	79.40%	20.60%	0.00%	0.00%	NA
Japonica Intermediate	241	90.50%	9.10%	0.00%	0.41%	NA
VI/Aromatic	96	83.30%	8.30%	0.00%	8.33%	NA
Intermediate	90	73.30%	16.70%	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
vg1218127576	A -> C	LOC_Os12g30200.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:32.163; most accessible tissue: Minghui63 young leaf, score: 54.11	N	N	N	N
vg1218127576	A -> DEL	N	N	silent_mutation	Average:32.163; most accessible tissue: Minghui63 young leaf, score: 54.11	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1218127576	NA	6.57E-11	mr1084	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
vg1218127576	2.19E-06	NA	mr1127	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
vg1218127576	NA	7.49E-06	mr1209	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
vg1218127576	NA	3.92E-07	mr1215	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
vg1218127576	NA	4.09E-07	mr1227	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
vg1218127576	2.52E-06	NA	mr1265	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
vg1218127576	4.64E-06	7.30E-06	mr1271	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
vg1218127576	1.26E-06	4.83E-06	mr1295	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
vg1218127576	NA	1.13E-15	mr1376	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
vg1218127576	NA	1.13E-15	mr1431	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
vg1218127576	NA	5.73E-07	mr1461	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
vg1218127576	NA	9.02E-08	mr1506	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
vg1218127576	NA	1.40E-06	mr1511	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
vg1218127576	1.26E-06	NA	mr1528	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
vg1218127576	4.59E-06	4.59E-06	mr1576	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
vg1218127576	6.30E-07	NA	mr1592	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
vg1218127576	NA	5.86E-08	mr1660	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
vg1218127576	NA	6.96E-06	mr1669	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
vg1218127576	NA	5.94E-07	mr1708	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
vg1218127576	NA	8.43E-06	mr1720	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
vg1218127576	NA	1.12E-07	mr1728	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
vg1218127576	NA	4.20E-07	mr1764	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
vg1218127576	9.10E-06	7.64E-12	mr1775	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
vg1218127576	NA	9.75E-07	mr1797	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
vg1218127576	NA	9.75E-07	mr1801	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
vg1218127576	NA	8.76E-09	mr1881	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
vg1218127576	NA	8.48E-06	mr1884	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