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Detailed information for vg1219213135:

Variant ID: vg1219213135 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 19213135
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.52, T: 0.48, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTTGAACCTAACATTATTCACAGCTTGAGAAAATTTGTTAGATAACAAAACCAAGTCCTCCTCCTCGAACTGTTCGAGTTGCTCATCGGACATGGCAT[C/T]
AAATAAAGCAAGCACAGAAGACTTCGATGAAGAAGCACCAACATCCAAAGAAGTCGAGGAAGAAACCAAAGCACTTGACTTAGAATCAATTTTACGAGAA

Reverse complement sequence

TTCTCGTAAAATTGATTCTAAGTCAAGTGCTTTGGTTTCTTCCTCGACTTCTTTGGATGTTGGTGCTTCTTCATCGAAGTCTTCTGTGCTTGCTTTATTT[G/A]
ATGCCATGTCCGATGAGCAACTCGAACAGTTCGAGGAGGAGGACTTGGTTTTGTTATCTAACAAATTTTCTCAAGCTGTGAATAATGTTAGGTTCAAGAA

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	37.20%	4.50%	11.79%	46.57%	NA
All Indica	2759	5.20%	6.10%	17.58%	71.08%	NA
All Japonica	1512	96.90%	0.10%	0.07%	2.91%	NA
Aus	269	1.90%	13.80%	22.30%	62.08%	NA
Indica I	595	6.40%	0.30%	14.29%	78.99%	NA
Indica II	465	4.30%	18.10%	18.06%	59.57%	NA
Indica III	913	2.40%	5.80%	18.29%	73.49%	NA
Indica Intermediate	786	8.10%	3.80%	18.96%	69.08%	NA
Temperate Japonica	767	98.70%	0.00%	0.00%	1.30%	NA
Tropical Japonica	504	97.60%	0.00%	0.20%	2.18%	NA
Japonica Intermediate	241	89.60%	0.80%	0.00%	9.54%	NA
VI/Aromatic	96	84.40%	3.10%	4.17%	8.33%	NA
Intermediate	90	68.90%	0.00%	7.78%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1219213135	C -> DEL	LOC_Os12g31900.1	N	frameshift_variant	Average:9.03; most accessible tissue: Minghui63 panicle, score: 16.27	N	N	N	N
vg1219213135	C -> T	LOC_Os12g31900.1	missense_variant ; p.Asp212Asn; MODERATE	nonsynonymous_codon ; D212N	Average:9.03; most accessible tissue: Minghui63 panicle, score: 16.27	benign	-1.29	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1219213135	9.65E-07	2.29E-08	mr1268	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
vg1219213135	6.64E-06	2.11E-07	mr1268	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