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Detailed information for vg0713262986:

Variant ID: vg0713262986 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13262986
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTATCACCAGAATTTTCATCTGGTGCTACCACGGTCTGAGTCACAGGTACAACACGAGTTACCAAATTTATTGGAATATTATTCTCTAGGATTTCCGGTG[T/C]
AACGTTAGCCCGAATTTCCTCAAGATTAATTTCCCTTTCCTGTGAGCTCCCCCAGACTTCATTATTTTCTAAGAATACGGCGTGTCTAGTTTCCACAAAT

Reverse complement sequence

ATTTGTGGAAACTAGACACGCCGTATTCTTAGAAAATAATGAAGTCTGGGGGAGCTCACAGGAAAGGGAAATTAATCTTGAGGAAATTCGGGCTAACGTT[A/G]
CACCGGAAATCCTAGAGAATAATATTCCAATAAATTTGGTAACTCGTGTTGTACCTGTGACTCAGACCGTGGTAGCACCAGATGAAAATTCTGGTGATAC

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	61.20%	18.70%	19.74%	0.36%	NA
All Indica	2759	47.30%	28.60%	24.07%	0.04%	NA
All Japonica	1512	91.50%	0.30%	7.47%	0.66%	NA
Aus	269	37.20%	29.40%	31.60%	1.86%	NA
Indica I	595	30.30%	36.30%	33.45%	0.00%	NA
Indica II	465	34.00%	42.60%	23.44%	0.00%	NA
Indica III	913	60.70%	19.40%	19.93%	0.00%	NA
Indica Intermediate	786	52.40%	25.30%	22.14%	0.13%	NA
Temperate Japonica	767	86.40%	0.40%	11.86%	1.30%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	90.50%	0.40%	9.13%	0.00%	NA
VI/Aromatic	96	42.70%	0.00%	56.25%	1.04%	NA
Intermediate	90	67.80%	13.30%	18.89%	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
vg0713262986	T -> DEL	LOC_Os07g23480.1	N	frameshift_variant	Average:14.347; most accessible tissue: Callus, score: 34.284	N	N	N	N
vg0713262986	T -> C	LOC_Os07g23480.1	missense_variant ; p.Thr1458Ala; MODERATE	nonsynonymous_codon ; T1458A	Average:14.347; most accessible tissue: Callus, score: 34.284	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713262986	1.21E-06	1.21E-06	mr1540	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
vg0713262986	NA	1.15E-06	mr1662_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