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Detailed information for vg0401597768:

Variant ID: vg0401597768 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1597768
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 47. )

Flanking Sequence (100 bp) in Reference Genome:

CTGGAAAAACACCTTTAAGTCCTGGCCCTCCCTTGAGAAAAGCTGGCCTGTATGGTATATTCTCCTGCCAACTGACTGATCACCAACAACGAATCACCCA[C/T]
AATTTCAATAGCATCGGCTTCAACCTCCTGAAGCAATTGTAACCCTTTTAAAACTACCTCATATTTAGCCTGATTATTAGTCACATGATGTTTAACAGCA

Reverse complement sequence

TGCTGTTAAACATCATGTGACTAATAATCAGGCTAAATATGAGGTAGTTTTAAAAGGGTTACAATTGCTTCAGGAGGTTGAAGCCGATGCTATTGAAATT[G/A]
TGGGTGATTCGTTGTTGGTGATCAGTCAGTTGGCAGGAGAATATACCATACAGGCCAGCTTTTCTCAAGGGAGGGCCAGGACTTAAAGGTGTTTTTCCAG

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	74.20%	16.20%	2.20%	7.38%	NA
All Indica	2759	88.50%	6.60%	2.14%	2.75%	NA
All Japonica	1512	44.60%	36.30%	1.92%	17.20%	NA
Aus	269	90.70%	5.90%	2.23%	1.12%	NA
Indica I	595	77.30%	14.10%	2.52%	6.05%	NA
Indica II	465	95.10%	3.00%	0.86%	1.08%	NA
Indica III	913	93.10%	2.80%	1.75%	2.30%	NA
Indica Intermediate	786	87.90%	7.30%	3.05%	1.78%	NA
Temperate Japonica	767	13.60%	59.30%	1.83%	25.29%	NA
Tropical Japonica	504	90.70%	4.40%	1.19%	3.77%	NA
Japonica Intermediate	241	46.90%	29.90%	3.73%	19.50%	NA
VI/Aromatic	96	91.70%	4.20%	3.12%	1.04%	NA
Intermediate	90	66.70%	15.60%	7.78%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401597768	C -> DEL	LOC_Os04g03630.1	N	frameshift_variant	Average:27.569; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg0401597768	C -> T	LOC_Os04g03630.1	missense_variant ; p.Val1535Met; MODERATE	nonsynonymous_codon ; V1535M	Average:27.569; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	unknown	unknown	TOLERATED	1.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401597768	3.19E-06	NA	mr1530_2	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