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Detailed information for vg0207959950:

Variant ID: vg0207959950 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7959950
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCCGCCGCCGCCGGCGACGACGCGCTGCCGCTGCCCATGACACCGTCGTACTACCGCAAGTCGTGCCCAACACTCGAGGCCATCGTGCGCGGCACCATG[C/G]
TCAGTGCCATCAAAGCCGAGCGCCGGATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCCAGGTAGATGATCCTAGCTAAGCTTCATT

Reverse complement sequence

AATGAAGCTTAGCTAGGATCATCTACCTGGACGAAGCAGTCGTGGAAGAAGAGGCGGAGGATGGAGGCGCCCATCCGGCGCTCGGCTTTGATGGCACTGA[G/C]
CATGGTGCCGCGCACGATGGCCTCGAGTGTTGGGCACGACTTGCGGTAGTACGACGGTGTCATGGGCAGCGGCAGCGCGTCGTCGCCGGCGGCGGCGGAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.60%	31.20%	0.23%	0.00%	NA
All Indica	2759	94.50%	5.40%	0.11%	0.00%	NA
All Japonica	1512	16.50%	83.00%	0.53%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	98.50%	1.30%	0.17%	0.00%	NA
Indica II	465	97.00%	2.80%	0.22%	0.00%	NA
Indica III	913	91.20%	8.80%	0.00%	0.00%	NA
Indica Intermediate	786	93.60%	6.20%	0.13%	0.00%	NA
Temperate Japonica	767	10.40%	89.20%	0.39%	0.00%	NA
Tropical Japonica	504	27.80%	71.80%	0.40%	0.00%	NA
Japonica Intermediate	241	12.00%	86.70%	1.24%	0.00%	NA
VI/Aromatic	96	60.40%	39.60%	0.00%	0.00%	NA
Intermediate	90	67.80%	32.20%	0.00%	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
vg0207959950	C -> G	LOC_Os02g14460.1	missense_variant ; p.Leu57Val; MODERATE	nonsynonymous_codon ; L57V	Average:73.146; most accessible tissue: Minghui63 root, score: 80.76	unknown	unknown	TOLERATED	0.34

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207959950	NA	4.87E-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
vg0207959950	NA	3.55E-10	mr1232_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
vg0207959950	3.17E-06	NA	mr1480_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
vg0207959950	NA	1.56E-06	mr1558_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
vg0207959950	NA	5.59E-12	mr1853_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
vg0207959950	NA	5.88E-07	mr1911_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