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Detailed information for vg1216877905:

Variant ID: vg1216877905 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 16877905
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGTGCATTCATGAACGCAATTTCGCAGAAGGTCATCGATCCGGATAGATTAGAAGCCCTTCAGAATGAAGTGGTGCAATGTCTCGTCAGTTTTGAGTTG[G/A]
TATTTCCACCTTCATTTTCAATATAATGACGCATCTGCTTTGTCACCTTGTGAAAGAGATCCGTATTCTCGGGCCTATGTACCTACACAACATGTTTCCT

Reverse complement sequence

AGGAAACATGTTGTGTAGGTACATAGGCCCGAGAATACGGATCTCTTTCACAAGGTGACAAAGCAGATGCGTCATTATATTGAAAATGAAGGTGGAAATA[C/T]
CAACTCAAAACTGACGAGACATTGCACCACTTCATTCTGAAGGGCTTCTAATCTATCCGGATCGATGACCTTCTGCGAAATTGCGTTCATGAATGCACAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	22.10%	0.50%	14.13%	63.27%	NA
All Indica	2759	9.70%	0.30%	19.17%	70.82%	NA
All Japonica	1512	48.10%	0.90%	6.08%	44.91%	NA
Aus	269	5.20%	0.00%	7.81%	86.99%	NA
Indica I	595	22.90%	0.00%	11.43%	65.71%	NA
Indica II	465	6.90%	0.00%	20.65%	72.47%	NA
Indica III	913	1.00%	0.70%	23.88%	74.48%	NA
Indica Intermediate	786	11.50%	0.40%	18.70%	69.47%	NA
Temperate Japonica	767	80.20%	1.60%	5.08%	13.17%	NA
Tropical Japonica	504	7.50%	0.00%	4.56%	87.90%	NA
Japonica Intermediate	241	31.10%	0.40%	12.45%	56.02%	NA
VI/Aromatic	96	2.10%	0.00%	17.71%	80.21%	NA
Intermediate	90	37.80%	1.10%	10.00%	51.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1216877905	G -> DEL	LOC_Os12g28560.1	N	splice_donor_variant	Average:8.988; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg1216877905	G -> A	LOC_Os12g28560.1	splice_donor_variant&intron_variant ; HIGH	splice_donor_variant	Average:8.988; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1216877905	9.40E-07	NA	mr1142	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
vg1216877905	NA	1.91E-14	mr1142	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
vg1216877905	NA	5.88E-08	mr1163	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
vg1216877905	NA	5.35E-06	mr1202	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
vg1216877905	1.25E-06	NA	mr1489	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
vg1216877905	3.61E-07	NA	mr1491	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
vg1216877905	7.53E-08	NA	mr1778	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
vg1216877905	NA	1.77E-07	mr1942	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
vg1216877905	NA	8.07E-07	mr1011_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
vg1216877905	NA	2.66E-08	mr1137_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
vg1216877905	NA	7.40E-09	mr1189_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
vg1216877905	NA	7.48E-06	mr1268_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
vg1216877905	NA	2.94E-10	mr1530_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