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Detailed information for vg1211588230:

Variant ID: vg1211588230 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 11588230
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

TTGATTGGAAACCGTCCTCGGTTTCACCTTGTCATGGAGCGTATTGTACTTATCTTTGTCTATCACAACATCCTGTGCTGAACATTTCTTGATGACCATA[T/C]
GATTGGATCCTAAAATCTTTGTAGTCGAAAAACTACAACACTCCCCTTCTTGCAAACCAACCTGTAACTCATTTAAACAACTAGAGGAACTAGATAGATA

Reverse complement sequence

TATCTATCTAGTTCCTCTAGTTGTTTAAATGAGTTACAGGTTGGTTTGCAAGAAGGGGAGTGTTGTAGTTTTTCGACTACAAAGATTTTAGGATCCAATC[A/G]
TATGGTCATCAAGAAATGTTCAGCACAGGATGTTGTGATAGACAAAGATAAGTACAATACGCTCCATGACAAGGTGAAACCGAGGACGGTTTCCAATCAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	88.80%	8.50%	0.44%	2.26%	NA
All Indica	2759	88.00%	7.50%	0.65%	3.81%	NA
All Japonica	1512	88.30%	11.60%	0.07%	0.07%	NA
Aus	269	97.80%	1.90%	0.00%	0.37%	NA
Indica I	595	91.10%	4.90%	1.68%	2.35%	NA
Indica II	465	96.30%	2.80%	0.22%	0.65%	NA
Indica III	913	83.00%	9.70%	0.11%	7.12%	NA
Indica Intermediate	786	86.60%	9.70%	0.76%	2.93%	NA
Temperate Japonica	767	96.50%	3.40%	0.13%	0.00%	NA
Tropical Japonica	504	85.90%	14.10%	0.00%	0.00%	NA
Japonica Intermediate	241	67.20%	32.40%	0.00%	0.41%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	88.90%	8.90%	2.22%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1211588230	T -> C	LOC_Os12g19890.1	missense_variant ; p.His156Arg; MODERATE	nonsynonymous_codon ; H156R	Average:39.009; most accessible tissue: Zhenshan97 flag leaf, score: 68.703	unknown	unknown	TOLERATED	0.08
vg1211588230	T -> DEL	LOC_Os12g19890.1	N	frameshift_variant	Average:39.009; most accessible tissue: Zhenshan97 flag leaf, score: 68.703	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1211588230	5.17E-06	NA	mr1034	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
vg1211588230	NA	1.57E-08	mr1236	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
vg1211588230	NA	1.20E-06	mr1236	Jap_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
vg1211588230	NA	9.94E-08	mr1319	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
vg1211588230	NA	6.41E-07	mr1336	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
vg1211588230	NA	1.86E-06	mr1786	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
vg1211588230	NA	4.24E-07	mr1558_2	Jap_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