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Detailed information for vg0711021713:

Variant ID: vg0711021713 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 11021713
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGTTTACTTGAGAAGAAGGAGGATGAAGCACCTGGGATGACTAAAGATAGTTTGCAAGGTAAATTAAATGGTGTTGAGATAAATAAAGGTGAGTATACT[C/T]
AAGGTGAGCTACACATGTCCACTTTTCATGGTATAGTAGAGCAACCATTAGTGGAACCAACTGCTGAGATTCCTTTGTCACAAGTGGATTTATTTGCTGT

Reverse complement sequence

ACAGCAAATAAATCCACTTGTGACAAAGGAATCTCAGCAGTTGGTTCCACTAATGGTTGCTCTACTATACCATGAAAAGTGGACATGTGTAGCTCACCTT[G/A]
AGTATACTCACCTTTATTTATCTCAACACCATTTAATTTACCTTGCAAACTATCTTTAGTCATCCCAGGTGCTTCATCCTCCTTCTTCTCAAGTAAACTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.70%	27.00%	0.42%	8.91%	NA
All Indica	2759	96.80%	0.90%	0.18%	2.07%	NA
All Japonica	1512	1.90%	79.00%	0.60%	18.52%	NA
Aus	269	90.70%	4.50%	0.00%	4.83%	NA
Indica I	595	99.50%	0.20%	0.17%	0.17%	NA
Indica II	465	96.80%	3.00%	0.00%	0.22%	NA
Indica III	913	99.80%	0.10%	0.00%	0.11%	NA
Indica Intermediate	786	91.30%	1.30%	0.51%	6.87%	NA
Temperate Japonica	767	2.00%	65.80%	1.04%	31.16%	NA
Tropical Japonica	504	0.80%	98.60%	0.00%	0.60%	NA
Japonica Intermediate	241	4.10%	79.70%	0.41%	15.77%	NA
VI/Aromatic	96	19.80%	7.30%	4.17%	68.75%	NA
Intermediate	90	52.20%	40.00%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0711021713	C -> DEL	LOC_Os07g18640.1	N	frameshift_variant	Average:27.515; most accessible tissue: Callus, score: 45.572	N	N	N	N
vg0711021713	C -> T	LOC_Os07g18640.1	stop_gained ; p.Gln135*; HIGH	stop_gained	Average:27.515; most accessible tissue: Callus, score: 45.572	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0711021713	2.03E-06	2.22E-11	mr1578	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
vg0711021713	NA	6.51E-14	mr1592	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
vg0711021713	NA	2.23E-36	mr1828	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
vg0711021713	NA	1.82E-10	mr1905	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
vg0711021713	NA	9.89E-15	mr1579_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
vg0711021713	NA	9.85E-11	mr1986_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