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Detailed information for vg0601078672:

Variant ID: vg0601078672 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 1078672
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.58, T: 0.42, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

GTGACGGCCATGGTTTCCCCACGGGATAGCCTCCTCACGAAGTAGTCGCCGACCTCCGCCTCCGGGTTGGTCGTCCACTGCGTCGTCACCACCTGCATCA[T/C]
CTTCCCCGGCTGCAAGTCCGTGATGTTGGGCAAGTAGAAGAGGTTAGCCATGCTGATCACGCCGCCGCCGGAGACGGAGACGGCCAAGACGGCGACGGAC

Reverse complement sequence

GTCCGTCGCCGTCTTGGCCGTCTCCGTCTCCGGCGGCGGCGTGATCAGCATGGCTAACCTCTTCTACTTGCCCAACATCACGGACTTGCAGCCGGGGAAG[A/G]
TGATGCAGGTGGTGACGACGCAGTGGACGACCAACCCGGAGGCGGAGGTCGGCGACTACTTCGTGAGGAGGCTATCCCGTGGGGAAACCATGGCCGTCAC

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	55.10%	12.70%	0.93%	31.27%	NA
All Indica	2759	41.80%	11.80%	1.20%	45.20%	NA
All Japonica	1512	90.30%	3.90%	0.66%	5.16%	NA
Aus	269	8.20%	41.60%	0.00%	50.19%	NA
Indica I	595	69.90%	5.50%	0.17%	24.37%	NA
Indica II	465	60.90%	5.20%	1.94%	32.04%	NA
Indica III	913	14.10%	19.30%	1.20%	65.39%	NA
Indica Intermediate	786	41.30%	11.80%	1.53%	45.29%	NA
Temperate Japonica	767	92.60%	6.50%	0.78%	0.13%	NA
Tropical Japonica	504	84.50%	0.40%	0.79%	14.29%	NA
Japonica Intermediate	241	95.00%	2.90%	0.00%	2.07%	NA
VI/Aromatic	96	4.20%	94.80%	0.00%	1.04%	NA
Intermediate	90	64.40%	15.60%	1.11%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0601078672	T -> C	LOC_Os06g02930.1	missense_variant ; p.Met128Val; MODERATE	nonsynonymous_codon ; M128V	Average:74.29; most accessible tissue: Minghui63 young leaf, score: 83.907	unknown	unknown	TOLERATED	1.00
vg0601078672	T -> DEL	LOC_Os06g02930.1	N	frameshift_variant	Average:74.29; most accessible tissue: Minghui63 young leaf, score: 83.907	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0601078672	2.53E-06	9.62E-06	mr1137	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
vg0601078672	6.18E-07	2.35E-06	mr1519	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
vg0601078672	NA	9.75E-08	mr1585_2	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