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Detailed information for vg0432436067:

Variant ID: vg0432436067 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32436067
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.70, A: 0.29, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:

GGGTACCAGCACTATGTCCTGGGACTGGTACCGAGATCGCGGTTTCGTAGGAAGCGGTTCGCGCCGTTTTCCCTACGACACGCTCCTATCAGGTGCCGTT[A/G]
TACGGCGGTATCAGATTGGGGTGTGACAAGAGATGGTATCAGAGCATTAGTTGGCCCTAGGATCGAAACCCCTAAATAGGATGGCATTATCTGAATACAA

Reverse complement sequence

TTGTATTCAGATAATGCCATCCTATTTAGGGGTTTCGATCCTAGGGCCAACTAATGCTCTGATACCATCTCTTGTCACACCCCAATCTGATACCGCCGTA[T/C]
AACGGCACCTGATAGGAGCGTGTCGTAGGGAAAACGGCGCGAACCGCTTCCTACGAAACCGCGATCTCGGTACCAGTCCCAGGACATAGTGCTGGTACCC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.50%	0.50%	15.43%	41.56%	NA
All Indica	2759	22.70%	0.30%	21.46%	55.53%	NA
All Japonica	1512	80.00%	0.70%	6.42%	12.83%	NA
Aus	269	33.10%	0.40%	7.43%	59.11%	NA
Indica I	595	15.50%	0.20%	5.38%	78.99%	NA
Indica II	465	38.10%	0.40%	16.13%	45.38%	NA
Indica III	913	15.00%	0.30%	40.31%	44.36%	NA
Indica Intermediate	786	28.10%	0.30%	14.89%	56.74%	NA
Temperate Japonica	767	82.70%	0.10%	1.43%	15.78%	NA
Tropical Japonica	504	82.70%	2.00%	11.31%	3.97%	NA
Japonica Intermediate	241	66.00%	0.00%	12.03%	21.99%	NA
VI/Aromatic	96	29.20%	0.00%	10.42%	60.42%	NA
Intermediate	90	62.20%	3.30%	11.11%	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
vg0432436067	A -> DEL	LOC_Os04g54530.1	N	frameshift_variant	Average:8.367; most accessible tissue: Minghui63 panicle, score: 20.733	N	N	N	N
vg0432436067	A -> G	LOC_Os04g54530.1	missense_variant ; p.Ile30Val; MODERATE	nonsynonymous_codon ; I30V	Average:8.367; most accessible tissue: Minghui63 panicle, score: 20.733	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432436067	NA	1.16E-06	mr1090	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
vg0432436067	NA	4.75E-06	mr1094	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
vg0432436067	NA	2.78E-06	mr1111	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
vg0432436067	NA	2.24E-06	mr1211	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
vg0432436067	8.57E-06	1.26E-06	mr1068_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
vg0432436067	6.59E-06	6.13E-10	mr1090_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
vg0432436067	NA	2.09E-07	mr1094_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
vg0432436067	4.00E-06	4.00E-06	mr1111_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
vg0432436067	NA	6.38E-07	mr1211_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