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Detailed information for vg0702311705:

Variant ID: vg0702311705 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 2311705
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.09, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

CCAAGGTCCTCGCCAAGGTCATCGAATACTGCATCAAGCACGCCGCCGCCGGGGAGGAGGAGGAGAAGGATCTGAAGAGCTTCGACGCCGAGTTCATCGA[T/C]
GTGGACAAGAACATGCTGTACGACCTGCTCCTGGCGTCCAATTTCATGAACATCAAGAGCTTGCTGGATTTGTGCTGCCAGCACACGGCGAACCTGATCA

Reverse complement sequence

TGATCAGGTTCGCCGTGTGCTGGCAGCACAAATCCAGCAAGCTCTTGATGTTCATGAAATTGGACGCCAGGAGCAGGTCGTACAGCATGTTCTTGTCCAC[A/G]
TCGATGAACTCGGCGTCGAAGCTCTTCAGATCCTTCTCCTCCTCCTCCCCGGCGGCGGCGTGCTTGATGCAGTATTCGATGACCTTGGCGAGGACCTTGG

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	57.80%	41.80%	0.11%	0.32%	NA
All Indica	2759	86.60%	12.80%	0.14%	0.47%	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	95.60%	4.20%	0.00%	0.17%	NA
Indica II	465	50.80%	48.20%	0.22%	0.86%	NA
Indica III	913	98.60%	1.10%	0.00%	0.33%	NA
Indica Intermediate	786	87.20%	11.80%	0.38%	0.64%	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	41.10%	55.60%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0702311705	T -> DEL	LOC_Os07g05180.1	N	frameshift_variant	Average:65.02; most accessible tissue: Zhenshan97 panicle, score: 80.486	N	N	N	N
vg0702311705	T -> C	LOC_Os07g05180.1	synonymous_variant ; p.Asp96Asp; LOW	synonymous_codon	Average:65.02; most accessible tissue: Zhenshan97 panicle, score: 80.486	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0702311705	NA	1.76E-06	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
vg0702311705	NA	1.53E-11	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
vg0702311705	NA	4.82E-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
vg0702311705	NA	8.04E-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
vg0702311705	NA	2.39E-14	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
vg0702311705	NA	8.37E-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
vg0702311705	NA	1.92E-10	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
vg0702311705	NA	1.38E-18	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
vg0702311705	NA	1.26E-11	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
vg0702311705	NA	9.18E-12	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
vg0702311705	NA	7.40E-08	mr1645_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
vg0702311705	NA	2.23E-07	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
vg0702311705	NA	4.81E-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