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Detailed information for vg1221437756:

Variant ID: vg1221437756 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 21437756
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCAAACTTAGGGATGTGCAATGCGTTACCGGTTGCATGGCCGCCCTAAGTCGTTTCATATCAAGGCTGGGAGAGAAGGCGCTACCCTTGTTTAAGCTCCT[C/T]
AAGCGCTCGGGACCGTTTACTTGGACGGAGGAAGCTGAACATGCCCTCACTCGGTTAAAGGCATATCTCAGCTCTCCCCCGGTTCTAGTCGCCCCGGAGC

Reverse complement sequence

GCTCCGGGGCGACTAGAACCGGGGGAGAGCTGAGATATGCCTTTAACCGAGTGAGGGCATGTTCAGCTTCCTCCGTCCAAGTAAACGGTCCCGAGCGCTT[G/A]
AGGAGCTTAAACAAGGGTAGCGCCTTCTCTCCCAGCCTTGATATGAAACGACTTAGGGCGGCCATGCAACCGGTAACGCATTGCACATCCCTAAGTTTGC

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	69.40%	1.50%	6.73%	22.41%	NA
All Indica	2759	66.50%	0.10%	8.41%	25.01%	NA
All Japonica	1512	82.30%	4.30%	2.84%	10.58%	NA
Aus	269	25.70%	0.00%	12.64%	61.71%	NA
Indica I	595	68.70%	0.00%	9.92%	21.34%	NA
Indica II	465	71.40%	0.20%	3.44%	24.95%	NA
Indica III	913	60.90%	0.00%	10.51%	28.59%	NA
Indica Intermediate	786	68.30%	0.30%	7.76%	23.66%	NA
Temperate Japonica	767	79.70%	8.20%	3.91%	8.21%	NA
Tropical Japonica	504	82.30%	0.20%	1.59%	15.87%	NA
Japonica Intermediate	241	90.50%	0.40%	2.07%	7.05%	NA
VI/Aromatic	96	63.50%	0.00%	6.25%	30.21%	NA
Intermediate	90	77.80%	3.30%	3.33%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1221437756	C -> DEL	LOC_Os12g35280.1	N	frameshift_variant	Average:43.333; most accessible tissue: Zhenshan97 flag leaf, score: 65.82	N	N	N	N
vg1221437756	C -> T	LOC_Os12g35280.1	synonymous_variant ; p.Leu1095Leu; LOW	synonymous_codon	Average:43.333; most accessible tissue: Zhenshan97 flag leaf, score: 65.82	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1221437756	1.23E-10	1.83E-11	mr1588_2	Jap_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