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Table 1 Enumeration of SNPs detected between Arabidopsis accessions Ws-2 and Col-0, according to chromosome

From: Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis

  Intragenic SNPs    
  Coding sequence Non-coding sequence   Total SNPs
Chromosome Synonymous Non-synonymous Stop created Stop deleted Unclassifiable Pseudogene Intronic Intergenic SNPs Apparenta Actualb
Chr1 8,559 6,608 54 19 4 25 10,144 14,292 39,705 37,381
Chr2 4,091 3,394 33 10 0 10 5,125 11,661 24,324 23,134
Chr3 6,141 4,945 36 6 7 11 7,341 13,607 32,094 30,496
Chr4 4,055 3,219 17 9 37 8 4,468 7,787 19,600 18,498
Chr5 7,810 5,924 35 15 6 18 9,062 14,309 37,179 35,278
Total (%) 30,656 (20.04) 24,090 (15.76) 175 (0.11) 59 (0.04) 54 (0.03) 72 (0.05) 36,140 (23.64) 61,656 (40.32) 152,902 (100.0) 144,787
  1. Protein coding gene locations were extracted from the latest TAIR 8 genome release, with information extracted from TIGR xml formatted files cross-referenced with FASTA formatted sequence files. SNPs within coding sequence (CDS) regions were classified as either synonymous (silent) or non-synonymous (amino acid changing) mutations, or as causing the creation or deletion of stop codons. In 11 instances, across the entire genome, inconsistency in the documented CDS locations prevented unambiguous classification of SNPs falling within these CDS regions; such SNPs are recorded under the category 'unclassifiable'. Similarly, SNPs falling within transcriptional units marked as pseudogenes could not be classified. All other SNPs falling within documented transcriptional units, but outside of specified CDS regions, are marked as intronic. All SNPs located out of the documented transcriptional units are classified as intergenic. aApparent number of SNPs based on the fact that splice variation means some SNPs will be scored twice. bActual number of SNPs.