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Detailed information for vg0702315769:

Variant ID: vg0702315769 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 2315769
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.29, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

GATGATCCTGGAAATGATAGACCTCCACTAAGCATATTGTCGTGGATGTAGAGCTCTTGCAGCATGGACGAAGTGAGTAAATTAGCAGGAATAGGACCTC[T/C]
GAACTGATTGGAGCTGAGATCAAGGACAGTGAGTTTGGGGTACTGAACAACAGCTTCAGGGATGGTGTCAGCTAGGGAATTATGGGAAAGATTCAGGTAG

Reverse complement sequence

CTACCTGAATCTTTCCCATAATTCCCTAGCTGACACCATCCCTGAAGCTGTTGTTCAGTACCCCAAACTCACTGTCCTTGATCTCAGCTCCAATCAGTTC[A/G]
GAGGTCCTATTCCTGCTAATTTACTCACTTCGTCCATGCTGCAAGAGCTCTACATCCACGACAATATGCTTAGTGGAGGTCTATCATTTCCAGGATCATC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	57.60%	41.90%	0.40%	0.11%	NA
All Indica	2759	86.40%	12.90%	0.58%	0.18%	NA
All Japonica	1512	0.90%	99.10%	0.00%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	95.10%	4.20%	0.67%	0.00%	NA
Indica II	465	50.10%	48.80%	0.86%	0.22%	NA
Indica III	913	98.60%	1.10%	0.22%	0.11%	NA
Indica Intermediate	786	87.00%	11.80%	0.76%	0.38%	NA
Temperate Japonica	767	0.00%	100.00%	0.00%	0.00%	NA
Tropical Japonica	504	2.80%	97.20%	0.00%	0.00%	NA
Japonica Intermediate	241	0.00%	100.00%	0.00%	0.00%	NA
VI/Aromatic	96	27.10%	72.90%	0.00%	0.00%	NA
Intermediate	90	36.70%	60.00%	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
vg0702315769	T -> DEL	LOC_Os07g05190.1	N	frameshift_variant	Average:45.744; most accessible tissue: Callus, score: 77.773	N	N	N	N
vg0702315769	T -> C	LOC_Os07g05190.1	missense_variant ; p.Arg470Gly; MODERATE	nonsynonymous_codon ; R470G	Average:45.744; most accessible tissue: Callus, score: 77.773	benign	-0.087	TOLERATED	0.15

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0702315769	NA	7.29E-07	mr1004	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
vg0702315769	NA	7.63E-12	mr1005	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
vg0702315769	NA	2.12E-14	mr1059	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
vg0702315769	NA	8.42E-15	mr1146	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
vg0702315769	NA	1.43E-22	mr1150	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
vg0702315769	NA	5.12E-13	mr1441	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
vg0702315769	NA	1.08E-14	mr1675	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
vg0702315769	NA	9.84E-15	mr1874	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
vg0702315769	NA	3.22E-15	mr1950	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
vg0702315769	NA	2.38E-09	mr1158_2	Ind_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
vg0702315769	NA	6.60E-19	mr1195_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
vg0702315769	NA	1.57E-10	mr1383_2	Ind_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
vg0702315769	NA	1.37E-11	mr1520_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
vg0702315769	NA	8.20E-08	mr1654_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
vg0702315769	NA	1.14E-19	mr1874_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