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Detailed information for vg0901482230:

Variant ID: vg0901482230 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 1482230
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, C: 0.02, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

GCTGGCACAATCTCTATCTTGTCGCCTTGCCATTGAATCAAGCATTGATGCATAGTCAAAGGAATGCAACAATTGGCGTGAATCCAATCCCTTCCAAGCA[C/A]
CAAACTGTACGAACCCTTCCCATCGATGACAAAAAACGTGGTAGGAATAGTCTTACTGCCGACTGTCAGCTCCACATTCAGAACACCTTTGGTTTCCGAT

Reverse complement sequence

ATCGGAAACCAAAGGTGTTCTGAATGTGGAGCTGACAGTCGGCAGTAAGACTATTCCTACCACGTTTTTTGTCATCGATGGGAAGGGTTCGTACAGTTTG[G/T]
TGCTTGGAAGGGATTGGATTCACGCCAATTGTTGCATTCCTTTGACTATGCATCAATGCTTGATTCAATGGCAAGGCGACAAGATAGAGATTGTGCCAGC

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	66.40%	22.10%	7.30%	4.21%	NA
All Indica	2759	96.80%	1.80%	1.16%	0.25%	NA
All Japonica	1512	7.10%	64.60%	16.80%	11.57%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	94.60%	4.40%	1.01%	0.00%	NA
Indica II	465	98.90%	0.90%	0.22%	0.00%	NA
Indica III	913	98.60%	0.10%	0.66%	0.66%	NA
Indica Intermediate	786	95.20%	2.30%	2.42%	0.13%	NA
Temperate Japonica	767	1.70%	96.90%	1.17%	0.26%	NA
Tropical Japonica	504	14.90%	22.20%	34.52%	28.37%	NA
Japonica Intermediate	241	7.90%	50.20%	29.46%	12.45%	NA
VI/Aromatic	96	40.60%	1.00%	43.75%	14.58%	NA
Intermediate	90	57.80%	21.10%	17.78%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0901482230	C -> DEL	LOC_Os09g03110.1	N	frameshift_variant	Average:43.448; most accessible tissue: Zhenshan97 flag leaf, score: 67.785	N	N	N	N
vg0901482230	C -> A	LOC_Os09g03110.1	missense_variant ; p.Val1169Leu; MODERATE	nonsynonymous_codon ; V1169L	Average:43.448; most accessible tissue: Zhenshan97 flag leaf, score: 67.785	benign	-1.335	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0901482230	NA	2.31E-35	Grain_thickness	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0901482230	NA	1.90E-13	Grain_thickness	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0901482230	NA	5.34E-12	Grain_width	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0901482230	4.99E-07	NA	mr1221	Jap_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
vg0901482230	NA	4.38E-15	mr1228	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
vg0901482230	NA	2.31E-06	mr1422	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
vg0901482230	NA	6.25E-08	mr1552	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
vg0901482230	NA	2.01E-07	mr1916	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
vg0901482230	NA	7.19E-06	mr1153_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
vg0901482230	NA	4.13E-07	mr1551_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
vg0901482230	NA	6.01E-10	mr1552_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
vg0901482230	NA	1.10E-07	mr1578_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
vg0901482230	NA	8.80E-08	mr1606_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
vg0901482230	NA	1.51E-18	mr1980_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