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Detailed information for vg0142999531:

Variant ID: vg0142999531 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 42999531
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

ACGTAACTACTGTGACCCGATGCGCCTGGAAATAATGGCGCAGTTTCCTCGAGGCCATTAGAATAGCGTAAAGCATCTTCTGGGCCTGAGGGTATCGGGT[T/C]
TTGGCGTCCCGGAGGGCCTCACTAACAAAGTAGACGGGCCGCTGCACCTTTCGGTGGGGCCGATCCTCTTCGCTAGGGGCCGCATCCCTGGGGCACTCTT

Reverse complement sequence

AAGAGTGCCCCAGGGATGCGGCCCCTAGCGAAGAGGATCGGCCCCACCGAAAGGTGCAGCGGCCCGTCTACTTTGTTAGTGAGGCCCTCCGGGACGCCAA[A/G]
ACCCGATACCCTCAGGCCCAGAAGATGCTTTACGCTATTCTAATGGCCTCGAGGAAACTGCGCCATTATTTCCAGGCGCATCGGGTCACAGTAGTTACGT

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	0.60%	0.10%	3.64%	95.68%	NA
All Indica	2759	0.50%	0.10%	1.27%	98.08%	NA
All Japonica	1512	0.00%	0.10%	5.89%	94.05%	NA
Aus	269	4.80%	0.00%	15.61%	79.55%	NA
Indica I	595	0.70%	0.20%	0.50%	98.66%	NA
Indica II	465	0.00%	0.00%	0.22%	99.78%	NA
Indica III	913	0.80%	0.10%	2.41%	96.71%	NA
Indica Intermediate	786	0.50%	0.10%	1.15%	98.22%	NA
Temperate Japonica	767	0.00%	0.10%	10.82%	89.05%	NA
Tropical Japonica	504	0.00%	0.00%	0.40%	99.60%	NA
Japonica Intermediate	241	0.00%	0.00%	1.66%	98.34%	NA
VI/Aromatic	96	0.00%	0.00%	0.00%	100.00%	NA
Intermediate	90	0.00%	0.00%	6.67%	93.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0142999531	T -> DEL	LOC_Os01g74230.1	N	frameshift_variant	Average:7.978; most accessible tissue: Callus, score: 15.971	N	N	N	N
vg0142999531	T -> C	LOC_Os01g74230.1	synonymous_variant ; p.Lys1157Lys; LOW	synonymous_codon	Average:7.978; most accessible tissue: Callus, score: 15.971	N	N	N	N