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Detailed information for vg1013475370:

Variant ID: vg1013475370 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 13475370
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, A: 0.14, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

AGCTATTAGTGGACAAGGAGATGGCGTCAGGAGTGCCCACAGTCCACCACCCAAACCAGCTGTGTCAAGCATGTCTGGTGGCGAAACAAGTCCGGCAGCC[G/A]
TTCCCAGGAATGGCAAACTATCGAGCAGAGGCGCCGCTCGAGCTGCTCCACATGGATCTGTGTGGGCCGATCACTCCATCGACGTTCGCCGGTAATCGAT

Reverse complement sequence

ATCGATTACCGGCGAACGTCGATGGAGTGATCGGCCCACACAGATCCATGTGGAGCAGCTCGAGCGGCGCCTCTGCTCGATAGTTTGCCATTCCTGGGAA[C/T]
GGCTGCCGGACTTGTTTCGCCACCAGACATGCTTGACACAGCTGGTTTGGGTGGTGGACTGTGGGCACTCCTGACGCCATCTCCTTGTCCACTAATAGCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.20%	24.60%	25.60%	14.58%	NA
All Indica	2759	39.40%	1.00%	40.01%	19.57%	NA
All Japonica	1512	28.50%	67.70%	2.65%	1.19%	NA
Aus	269	41.60%	0.40%	15.24%	42.75%	NA
Indica I	595	47.20%	0.00%	49.08%	3.70%	NA
Indica II	465	48.00%	2.80%	35.70%	13.55%	NA
Indica III	913	29.10%	0.40%	35.93%	34.50%	NA
Indica Intermediate	786	40.30%	1.40%	40.46%	17.81%	NA
Temperate Japonica	767	5.60%	94.10%	0.26%	0.00%	NA
Tropical Japonica	504	58.90%	34.10%	3.97%	2.98%	NA
Japonica Intermediate	241	37.80%	53.50%	7.47%	1.24%	NA
VI/Aromatic	96	9.40%	79.20%	4.17%	7.29%	NA
Intermediate	90	27.80%	38.90%	23.33%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1013475370	G -> A	LOC_Os10g26030.1	synonymous_variant ; p.Pro388Pro; LOW	synonymous_codon	Average:45.921; most accessible tissue: Minghui63 young leaf, score: 64.378	N	N	N	N
vg1013475370	G -> DEL	LOC_Os10g26030.1	N	frameshift_variant	Average:45.921; most accessible tissue: Minghui63 young leaf, score: 64.378	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1013475370	NA	4.04E-07	mr1022	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
vg1013475370	5.83E-06	2.16E-08	mr1424	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
vg1013475370	NA	9.40E-06	mr1450	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
vg1013475370	NA	9.25E-06	mr1511	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
vg1013475370	2.02E-11	7.57E-48	mr1533	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
vg1013475370	9.26E-13	3.92E-22	mr1533	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
vg1013475370	NA	2.19E-06	mr1881	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
vg1013475370	NA	5.62E-08	mr1884	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
vg1013475370	2.38E-09	3.02E-43	mr1980	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
vg1013475370	6.13E-10	2.99E-25	mr1980	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
vg1013475370	NA	9.24E-08	mr1156_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
vg1013475370	4.06E-11	3.67E-47	mr1533_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
vg1013475370	2.82E-11	2.34E-26	mr1533_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
vg1013475370	7.25E-09	5.26E-25	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
vg1013475370	6.05E-06	2.97E-11	mr1980_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