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Detailed information for vg0719817684:

Variant ID: vg0719817684 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 19817684
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTCGCAGTTCTGGGGCTGAAAGGGCCTCTCATGATTTCCCTGTTGGATCTCGTGAGAATCCCGTTCGGCTCTACAAGACTCTTGGATTTGACACCACTC[C/T]
TATGCACCACATTGGAAGACCCAAGTCCAACTACCTTCATCAGCTTGCCACCAACTACCTTCATCAGCTTGCCAAGTGCAGAAGGGACCGTTTGATTGAT

Reverse complement sequence

ATCAATCAAACGGTCCCTTCTGCACTTGGCAAGCTGATGAAGGTAGTTGGTGGCAAGCTGATGAAGGTAGTTGGACTTGGGTCTTCCAATGTGGTGCATA[G/A]
GAGTGGTGTCAAATCCAAGAGTCTTGTAGAGCCGAACGGGATTCTCACGAGATCCAACAGGGAAATCATGAGAGGCCCTTTCAGCCCCAGAACTGCGACC

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	44.90%	5.10%	9.37%	40.56%	NA
All Indica	2759	14.60%	7.40%	9.89%	68.10%	NA
All Japonica	1512	88.20%	1.60%	9.66%	0.53%	NA
Aus	269	88.80%	2.60%	3.72%	4.83%	NA
Indica I	595	8.60%	3.90%	9.41%	78.15%	NA
Indica II	465	10.80%	6.20%	10.11%	72.90%	NA
Indica III	913	19.80%	10.30%	10.51%	59.36%	NA
Indica Intermediate	786	15.50%	7.30%	9.41%	67.81%	NA
Temperate Japonica	767	96.60%	1.20%	1.30%	0.91%	NA
Tropical Japonica	504	71.20%	2.40%	26.39%	0.00%	NA
Japonica Intermediate	241	97.10%	1.20%	1.24%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	56.70%	10.00%	14.44%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0719817684	C -> DEL	LOC_Os07g33190.1	N	frameshift_variant	Average:11.895; most accessible tissue: Callus, score: 26.926	N	N	N	N
vg0719817684	C -> T	LOC_Os07g33190.1	missense_variant ; p.Pro542Leu; MODERATE	nonsynonymous_codon ; P542L	Average:11.895; most accessible tissue: Callus, score: 26.926	unknown	unknown	TOLERATED	0.29

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0719817684	2.94E-07	NA	mr1092	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