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Detailed information for vg0320570289:

Variant ID: vg0320570289 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 20570289
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACCACCACCGGGCGGTAACAGCATGATCATGCCGAGCTCCCTAACTACAGCCGGCACGTCTCAGAGCCCGCCTGACGCCACCACCGCCGGCGCACCACCA[C/A]
CTCCGGCTCCATCGGTGGGAGCATGGGGCGGCAACGTGCCGAGCGGGTTGCTCATCGGTGTCGCCTTCGCCGGTTTCCTCCTGGCGTTGGCGTCCATGTT

Reverse complement sequence

AACATGGACGCCAACGCCAGGAGGAAACCGGCGAAGGCGACACCGATGAGCAACCCGCTCGGCACGTTGCCGCCCCATGCTCCCACCGATGGAGCCGGAG[G/T]
TGGTGGTGCGCCGGCGGTGGTGGCGTCAGGCGGGCTCTGAGACGTGCCGGCTGTAGTTAGGGAGCTCGGCATGATCATGCTGTTACCGCCCGGTGGTGGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.50% 0.40% 0.08% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 98.50% 1.30% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 95.60% 4.00% 0.40% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0320570289 C -> A LOC_Os03g37120.1 missense_variant ; p.Pro233Thr; MODERATE nonsynonymous_codon ; P233T Average:76.904; most accessible tissue: Zhenshan97 panicle, score: 89.623 unknown unknown TOLERATED 0.23