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Detailed information for vg1202110385:

Variant ID: vg1202110385 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 2110385
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

CCGTACAGGATGGCGGCCAACGAACTAGCAAAGGTCAAGAAGCAGGTTGATGAGCAGCTGCAGAAAGGGTACATACGACCAAGTACTTCACCTTGGGGTG[C/T]
TCCGGTCATTTTTGTGGAGAAAAAGGATAAGACGAAGAGGATGTGCGTTGATTATCGCGCACTCAATGAGGTCACAATCAAGAATAAATATCCTTTACCG

Reverse complement sequence

CGGTAAAGGATATTTATTCTTGATTGTGACCTCATTGAGTGCGCGATAATCAACGCACATCCTCTTCGTCTTATCCTTTTTCTCCACAAAAATGACCGGA[G/A]
CACCCCAAGGTGAAGTACTTGGTCGTATGTACCCTTTCTGCAGCTGCTCATCAACCTGCTTCTTGACCTTTGCTAGTTCGTTGGCCGCCATCCTGTACGG

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	65.90%	15.70%	6.37%	12.00%	NA
All Indica	2759	52.30%	22.50%	9.39%	15.80%	NA
All Japonica	1512	82.70%	7.00%	2.38%	7.87%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	74.30%	4.40%	2.86%	18.49%	NA
Indica II	465	47.50%	16.60%	13.55%	22.37%	NA
Indica III	913	34.40%	42.30%	11.17%	12.16%	NA
Indica Intermediate	786	59.30%	16.80%	9.80%	14.12%	NA
Temperate Japonica	767	93.90%	0.10%	1.04%	4.95%	NA
Tropical Japonica	504	63.50%	20.60%	2.58%	13.29%	NA
Japonica Intermediate	241	87.60%	0.40%	6.22%	5.81%	NA
VI/Aromatic	96	89.60%	9.40%	1.04%	0.00%	NA
Intermediate	90	75.60%	6.70%	5.56%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1202110385	C -> DEL	LOC_Os12g04910.1	N	frameshift_variant	Average:18.889; most accessible tissue: Minghui63 panicle, score: 34.226	N	N	N	N
vg1202110385	C -> T	LOC_Os12g04910.1	missense_variant ; p.Ala590Val; MODERATE	nonsynonymous_codon ; A590V	Average:18.889; most accessible tissue: Minghui63 panicle, score: 34.226	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1202110385	NA	5.19E-07	mr1113	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
vg1202110385	NA	4.58E-09	mr1114	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
vg1202110385	NA	2.46E-08	mr1116	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
vg1202110385	NA	6.22E-10	mr1118	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
vg1202110385	NA	1.07E-06	mr1247	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
vg1202110385	NA	5.25E-06	mr1261	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
vg1202110385	NA	2.34E-12	mr1495	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
vg1202110385	NA	2.69E-09	mr1794	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
vg1202110385	5.59E-06	1.24E-12	mr1113_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
vg1202110385	NA	3.75E-12	mr1114_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
vg1202110385	NA	1.83E-08	mr1117_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
vg1202110385	NA	1.82E-07	mr1119_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
vg1202110385	NA	2.39E-09	mr1120_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
vg1202110385	NA	2.93E-10	mr1247_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
vg1202110385	6.65E-06	4.54E-08	mr1258_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
vg1202110385	NA	1.52E-12	mr1794_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
vg1202110385	NA	8.36E-08	mr1961_2	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