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Detailed information for vg0233330713:

Variant ID: vg0233330713 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 33330713
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGACGGTGTCCGCCACGAGCGCGTGGCGGAAGCAGTTCACCCCCTCCCGCATCCCGCCGTCGAGGTAGTCGTACATCCGCGTCTCCTCGCCGTACCTGTT[A/C]
CTCCCCTTGCCGCCGCGGCGCAGCCACCGGCCGAACACCTCGTCCTCGGGCCCCTTCACGTCGCCCCGCAGCGCCTCCGTCGCCGCCACCCACGCCGCCA

Reverse complement sequence

TGGCGGCGTGGGTGGCGGCGACGGAGGCGCTGCGGGGCGACGTGAAGGGGCCCGAGGACGAGGTGTTCGGCCGGTGGCTGCGCCGCGGCGGCAAGGGGAG[T/G]
AACAGGTACGGCGAGGAGACGCGGATGTACGACTACCTCGACGGCGGGATGCGGGAGGGGGTGAACTGCTTCCGCCACGCGCTCGTGGCGGACACCGTCG

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 64.40% 35.50% 0.06% 0.00% NA
All Indica  2759 98.50% 1.40% 0.04% 0.00% NA
All Japonica  1512 1.00% 99.00% 0.00% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 97.20% 2.70% 0.13% 0.00% NA
Temperate Japonica  767 1.20% 98.80% 0.00% 0.00% NA
Tropical Japonica  504 0.00% 100.00% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 11.50% 88.50% 0.00% 0.00% NA
Intermediate  90 42.20% 55.60% 2.22% 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
vg0233330713 A -> C LOC_Os02g54390.1 missense_variant ; p.Ser240Arg; MODERATE nonsynonymous_codon ; S240R Average:81.804; most accessible tissue: Minghui63 root, score: 90.139 benign -1.363 TOLERATED 0.52