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Detailed information for vg0707566881:

Variant ID: vg0707566881 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 7566881
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: 0.08, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTCGGCCAAGCACTTTTGCTGATAGCCTTTGGCTCGGGGAAGAACAGACGCGAAGAGCAAATACTGTTCGACGTCGTCGACATCCCGTACAACTACAA[T/C]
GCCATCTTTGGCCGTGCAACCCTGAACAAGTTCGAAGCCATTTCCCACCACAATTATCTCAAGCTCAAGATGCCCAGCCCGACAGTGGTGATAGTAGTCA

Reverse complement sequence

TGACTACTATCACCACTGTCGGGCTGGGCATCTTGAGCTTGAGATAATTGTGGTGGGAAATGGCTTCGAACTTGTTCAGGGTTGCACGGCCAAAGATGGC[A/G]
TTGTAGTTGTACGGGATGTCGACGACGTCGAACAGTATTTGCTCTTCGCGTCTGTTCTTCCCCGAGCCAAAGGCTATCAGCAAAAGTGCTTGGCCGAGAA

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	57.00%	36.80%	0.91%	5.25%	NA
All Indica	2759	92.10%	6.80%	0.65%	0.40%	NA
All Japonica	1512	5.40%	79.00%	0.13%	15.48%	NA
Aus	269	5.60%	87.00%	7.43%	0.00%	NA
Indica I	595	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	91.40%	6.00%	1.08%	1.51%	NA
Indica III	913	97.50%	1.80%	0.44%	0.33%	NA
Indica Intermediate	786	81.30%	17.40%	1.15%	0.13%	NA
Temperate Japonica	767	1.20%	96.00%	0.00%	2.87%	NA
Tropical Japonica	504	12.10%	66.50%	0.40%	21.03%	NA
Japonica Intermediate	241	4.60%	51.50%	0.00%	43.98%	NA
VI/Aromatic	96	21.90%	77.10%	1.04%	0.00%	NA
Intermediate	90	40.00%	54.40%	2.22%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0707566881	T -> DEL	LOC_Os07g13190.1	N	frameshift_variant	Average:36.727; most accessible tissue: Zhenshan97 flag leaf, score: 60.705	N	N	N	N
vg0707566881	T -> C	LOC_Os07g13190.1	synonymous_variant ; p.Asn662Asn; LOW	synonymous_codon	Average:36.727; most accessible tissue: Zhenshan97 flag leaf, score: 60.705	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0707566881	NA	5.22E-06	mr1062	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
vg0707566881	2.44E-06	2.44E-06	mr1360	Ind_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
vg0707566881	1.27E-06	1.18E-06	mr1525	Ind_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
vg0707566881	NA	9.20E-06	mr1541	Ind_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
vg0707566881	NA	4.51E-06	mr1676	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
vg0707566881	NA	6.54E-06	mr1968	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