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Detailed information for vg0903875315:

Variant ID: vg0903875315 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 3875315
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:

ATAAGTCTTGTCCCAAAGATCCCTTCGGGTTGCCTCGCATTGACCAGGTAGTTGACTCAACCGCCGGCTGTGAGCTACTCAGCTTTTTGGATTGCTACTC[A/T]
GGATATCATCAGATCCGACTAAAGGAATCCGACTGCTTAAAGACTTCATTCATCACGCCCTTCGGGGCCTACTGCTACATCACCATACCTTTCGGATTAA

Reverse complement sequence

TTAATCCGAAAGGTATGGTGATGTAGCAGTAGGCCCCGAAGGGCGTGATGAATGAAGTCTTTAAGCAGTCGGATTCCTTTAGTCGGATCTGATGATATCC[T/A]
GAGTAGCAATCCAAAAAGCTGAGTAGCTCACAGCCGGCGGTTGAGTCAACTACCTGGTCAATGCGAGGCAACCCGAAGGGATCTTTGGGACAAGACTTAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.90%	12.40%	0.51%	0.19%	NA
All Indica	2759	99.50%	0.50%	0.00%	0.00%	NA
All Japonica	1512	64.60%	33.30%	1.59%	0.53%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.30%	0.70%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.80%	0.00%	0.00%	NA
Temperate Japonica	767	97.80%	2.10%	0.13%	0.00%	NA
Tropical Japonica	504	19.80%	74.20%	4.37%	1.59%	NA
Japonica Intermediate	241	52.30%	47.30%	0.41%	0.00%	NA
VI/Aromatic	96	57.30%	42.70%	0.00%	0.00%	NA
Intermediate	90	73.30%	25.60%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0903875315	A -> DEL	LOC_Os09g07680.1	N	frameshift_variant	Average:55.505; most accessible tissue: Zhenshan97 flag leaf, score: 81.41	N	N	N	N
vg0903875315	A -> T	LOC_Os09g07680.1	synonymous_variant ; p.Ser730Ser; LOW	synonymous_codon	Average:55.505; most accessible tissue: Zhenshan97 flag leaf, score: 81.41	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0903875315	NA	2.70E-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
vg0903875315	3.98E-09	NA	Grain_weight	All	YES	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
vg0903875315	NA	5.44E-07	mr1554	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
vg0903875315	NA	9.66E-07	mr1596	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
vg0903875315	NA	5.93E-06	mr1184_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
vg0903875315	NA	3.14E-07	mr1363_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
vg0903875315	NA	2.10E-07	mr1554_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
vg0903875315	NA	9.85E-06	mr1556_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
vg0903875315	NA	1.59E-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
vg0903875315	NA	3.41E-06	mr1582_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
vg0903875315	NA	9.13E-13	mr1593_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
vg0903875315	NA	2.07E-14	mr1864_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