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Detailed information for vg0412735652:

Variant ID: vg0412735652 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12735652
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCACAACAAACTTGTCCAGAAATTCCATGAACACTTTGTTCATCAGATTCATGAAGAATGCAGGTGCGTTGGTAAGTCCGAAAGACATAACCGTGCACTC[A/C]
TATAGCCCGTACCGGGTGGTGAAGGCCGTCTTTGGAATATCCTCTTCCCGAATCCTCAACTGGTGGTAGCCTGATCGCAGGTCTATCTTAGAAAACACTT

Reverse complement sequence

AAGTGTTTTCTAAGATAGACCTGCGATCAGGCTACCACCAGTTGAGGATTCGGGAAGAGGATATTCCAAAGACGGCCTTCACCACCCGGTACGGGCTATA[T/G]
GAGTGCACGGTTATGTCTTTCGGACTTACCAACGCACCTGCATTCTTCATGAATCTGATGAACAAAGTGTTCATGGAATTTCTGGACAAGTTTGTTGTGG

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	29.60%	9.40%	51.86%	9.10%	NA
All Indica	2759	8.30%	0.50%	78.72%	12.40%	NA
All Japonica	1512	68.50%	27.50%	3.70%	0.33%	NA
Aus	269	4.80%	0.00%	65.43%	29.74%	NA
Indica I	595	9.90%	0.20%	70.92%	18.99%	NA
Indica II	465	12.30%	1.30%	71.83%	14.62%	NA
Indica III	913	5.40%	0.30%	87.40%	6.90%	NA
Indica Intermediate	786	8.30%	0.60%	78.63%	12.47%	NA
Temperate Japonica	767	94.10%	2.50%	2.74%	0.65%	NA
Tropical Japonica	504	30.20%	65.70%	4.17%	0.00%	NA
Japonica Intermediate	241	66.80%	27.40%	5.81%	0.00%	NA
VI/Aromatic	96	85.40%	2.10%	11.46%	1.04%	NA
Intermediate	90	43.30%	14.40%	40.00%	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
vg0412735652	A -> C	LOC_Os04g22490.1	N	stop_gained	Average:10.391; most accessible tissue: Zhenshan97 flag leaf, score: 17.069	N	N	N	N
vg0412735652	A -> DEL	LOC_Os04g22490.1	N	frameshift_variant	Average:10.391; most accessible tissue: Zhenshan97 flag leaf, score: 17.069	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412735652	NA	1.61E-07	mr1077	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
vg0412735652	NA	3.21E-24	mr1301	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
vg0412735652	NA	1.54E-15	mr1410	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
vg0412735652	NA	1.67E-08	mr1539	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
vg0412735652	NA	3.30E-07	mr1668	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
vg0412735652	NA	7.78E-29	mr1699	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
vg0412735652	NA	4.02E-08	mr1993	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
vg0412735652	NA	1.14E-07	mr1993	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
vg0412735652	NA	6.59E-24	mr1301_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
vg0412735652	NA	3.32E-09	mr1398_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
vg0412735652	NA	1.99E-16	mr1410_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
vg0412735652	7.10E-06	NA	mr1850_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
vg0412735652	NA	4.02E-12	mr1993_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