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Detailed information for vg0900606355:

Variant ID: vg0900606355 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 606355
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: 322. )

Flanking Sequence (100 bp) in Reference Genome:

AACCGGTACATCTGTGTAGGTAGCTCTCTGATCTTATCAGGCGTGACTAGCAGTTCACCGAGTTTAAACGTGTACATGACCGGAGCCGTTTCGATAGGTG[C/T]
GTCCTCTAGCAACTGCTCCATACTCAGTCCCGTATCTTTCAAGAAGTTGCATATCTCTAGTTGTGCCGGTTCTACGATTAACGGTTCAACCTCTTGTCGT

Reverse complement sequence

ACGACAAGAGGTTGAACCGTTAATCGTAGAACCGGCACAACTAGAGATATGCAACTTCTTGAAAGATACGGGACTGAGTATGGAGCAGTTGCTAGAGGAC[G/A]
CACCTATCGAAACGGCTCCGGTCATGTACACGTTTAAACTCGGTGAACTGCTAGTCACGCCTGATAAGATCAGAGAGCTACCTACACAGATGTACCGGTT

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	70.00%	22.70%	3.09%	4.19%	NA
All Indica	2759	59.20%	37.20%	3.37%	0.18%	NA
All Japonica	1512	84.60%	0.30%	2.45%	12.70%	NA
Aus	269	80.70%	13.80%	5.58%	0.00%	NA
Indica I	595	64.70%	33.40%	1.85%	0.00%	NA
Indica II	465	80.00%	19.40%	0.65%	0.00%	NA
Indica III	913	47.50%	46.40%	5.70%	0.33%	NA
Indica Intermediate	786	56.40%	39.90%	3.44%	0.25%	NA
Temperate Japonica	767	72.10%	0.40%	4.30%	23.21%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	92.50%	0.00%	1.66%	5.81%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	5.60%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0900606355	C -> DEL	LOC_Os09g01900.1	N	frameshift_variant	Average:38.089; most accessible tissue: Zhenshan97 flag leaf, score: 73.119	N	N	N	N
vg0900606355	C -> T	LOC_Os09g01900.1	missense_variant ; p.Ala574Thr; MODERATE	nonsynonymous_codon ; A574T	Average:38.089; most accessible tissue: Zhenshan97 flag leaf, score: 73.119	unknown	unknown	DELETERIOUS	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900606355	4.12E-06	NA	mr1208	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