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Detailed information for vg0319300846:

Variant ID: vg0319300846 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 19300846
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAACATTAGGCAACGTGGCAACGCGCAAGACCCAAGGCTGCAGCAGGGAACAACTGTCGAAGCACCCCGCGAAGCAGTTCAAGAACAAACACCCCCGGTC[G/A]
AACAACGTCAAGACGTGCAACAAAGGGTAATCCAAGTGATTACGAGGGCCGACCCGCCAGGCCAATTATCTAAAAGGCAGAAAAAGATGCAGATCTGAGC

Reverse complement sequence

GCTCAGATCTGCATCTTTTTCTGCCTTTTAGATAATTGGCCTGGCGGGTCGGCCCTCGTAATCACTTGGATTACCCTTTGTTGCACGTCTTGACGTTGTT[C/T]
GACCGGGGGTGTTTGTTCTTGAACTGCTTCGCGGGGTGCTTCGACAGTTGTTCCCTGCTGCAGCCTTGGGTCTTGCGCGTTGCCACGTTGCCTAATGTTT

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	84.30%	12.50%	3.17%	0.02%	NA
All Indica	2759	95.80%	1.80%	2.39%	0.00%	NA
All Japonica	1512	65.90%	29.00%	5.03%	0.00%	NA
Aus	269	90.30%	7.80%	1.49%	0.37%	NA
Indica I	595	96.10%	1.50%	2.35%	0.00%	NA
Indica II	465	94.20%	1.30%	4.52%	0.00%	NA
Indica III	913	98.80%	1.10%	0.11%	0.00%	NA
Indica Intermediate	786	93.00%	3.20%	3.82%	0.00%	NA
Temperate Japonica	767	90.50%	4.40%	5.08%	0.00%	NA
Tropical Japonica	504	42.90%	54.40%	2.78%	0.00%	NA
Japonica Intermediate	241	36.10%	54.40%	9.54%	0.00%	NA
VI/Aromatic	96	32.30%	66.70%	1.04%	0.00%	NA
Intermediate	90	75.60%	21.10%	3.33%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0319300846	G -> A	LOC_Os03g33760.1	missense_variant ; p.Glu631Lys; MODERATE	nonsynonymous_codon ; E631K	Average:40.799; most accessible tissue: Minghui63 flag leaf, score: 61.847	benign	0.278	DELETERIOUS	0.05
vg0319300846	G -> DEL	LOC_Os03g33760.1	N	frameshift_variant	Average:40.799; most accessible tissue: Minghui63 flag leaf, score: 61.847	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0319300846	NA	2.07E-10	Grain_weight	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
vg0319300846	NA	3.14E-06	mr1040	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
vg0319300846	NA	4.75E-07	mr1045	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
vg0319300846	NA	9.35E-06	mr1213	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
vg0319300846	NA	2.94E-06	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
vg0319300846	NA	6.58E-06	mr1319	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
vg0319300846	NA	8.59E-06	mr1404	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
vg0319300846	5.17E-07	1.46E-06	mr1482	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
vg0319300846	NA	4.84E-07	mr1482	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
vg0319300846	NA	5.39E-06	mr1507	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
vg0319300846	NA	1.15E-06	mr1521	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
vg0319300846	NA	7.98E-06	mr1620	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
vg0319300846	NA	9.86E-08	mr1729	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
vg0319300846	NA	1.85E-07	mr1729	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
vg0319300846	NA	1.17E-16	mr1825	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