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Detailed information for vg1204312554:

Variant ID: vg1204312554 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4312554
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTTTGTCTTACAGCCGATCATTCCCAAGTCTTATAATTGCAGAAAAAGAAGACTGCGGTGAAGAAGAAATCGGCTGCAACAACATCTAAACCAGTTCCA[C/T]
CAGTAAGATAGTTTTAACTTTTATTAGTTAATTTTTTAGCCAATTCTGTCTGACACTTGTTTCCTTTCAGCCTTCACCTCCTCCTTCTCCTCCTGTACAA

Reverse complement sequence

TTGTACAGGAGGAGAAGGAGGAGGTGAAGGCTGAAAGGAAACAAGTGTCAGACAGAATTGGCTAAAAAATTAACTAATAAAAGTTAAAACTATCTTACTG[G/A]
TGGAACTGGTTTAGATGTTGTTGCAGCCGATTTCTTCTTCACCGCAGTCTTCTTTTTCTGCAATTATAAGACTTGGGAATGATCGGCTGTAAGACAAAAT

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	30.30%	19.10%	17.92%	32.75%	NA
All Indica	2759	14.00%	27.10%	24.54%	34.32%	NA
All Japonica	1512	56.70%	1.70%	7.14%	34.46%	NA
Aus	269	46.80%	40.10%	10.78%	2.23%	NA
Indica I	595	13.10%	16.30%	16.64%	53.95%	NA
Indica II	465	12.30%	30.30%	18.06%	39.35%	NA
Indica III	913	13.10%	32.20%	33.63%	21.03%	NA
Indica Intermediate	786	16.70%	27.60%	23.79%	31.93%	NA
Temperate Japonica	767	82.30%	1.00%	2.09%	14.60%	NA
Tropical Japonica	504	28.00%	3.00%	14.88%	54.17%	NA
Japonica Intermediate	241	35.30%	1.20%	7.05%	56.43%	NA
VI/Aromatic	96	27.10%	3.10%	12.50%	57.29%	NA
Intermediate	90	38.90%	16.70%	23.33%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204312554	C -> DEL	LOC_Os12g08500.1	N	frameshift_variant	Average:14.802; most accessible tissue: Callus, score: 28.566	N	N	N	N
vg1204312554	C -> T	LOC_Os12g08500.1	missense_variant&splice_region_variant ; p.Pro259Ser; MODERATE	nonsynonymous_codon ; P259S	Average:14.802; most accessible tissue: Callus, score: 28.566	unknown	unknown	TOLERATED	0.10

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204312554	1.04E-07	7.78E-08	mr1137	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